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Allman ES, Banos H, Rhodes JA. Testing Multispecies Coalescent Simulators Using Summary Statistics. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:1613-1618. [PMID: 35617176 PMCID: PMC10183998 DOI: 10.1109/tcbb.2022.3177956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
As genomic-scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process have become essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ensure that they give valid samples. This work develops methods for checking whether a collection of gene trees is in accord with the MSC model on a given species tree. When applied to well-known simulators, we find that several give flawed samples. The tests presented are capable of validating both topological and metric properties of gene tree samples, and are implemented in a freely available R package MSCsimtester so that developers and users may easily apply them.
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Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson R, Visagie C, Yilmaz N, Gené J, Cano J, Chen A, Nováková A, Yaguchi T, Kolařík M, Hubka V. Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Stud Mycol 2022; 102:53-93. [PMID: 36760461 PMCID: PMC9903908 DOI: 10.3114/sim.2022.102.02] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.
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Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding author: V. Hubka, ; F. Sklenář,
| | - K. Glässnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ž. Jurjević
- EMSL Analytical, Cinnaminson, New Jersey, USA
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Cano
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - A.J. Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, China
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;, Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan,*Corresponding author: V. Hubka, ; F. Sklenář,
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Glässnerová K, Sklenář F, Jurjević Ž, Houbraken J, Yaguchi T, Visagie C, Gené J, Siqueira J, Kubátová A, Kolařík M, Hubka V. A monograph of Aspergillus section Candidi. Stud Mycol 2022; 102:1-51. [PMID: 36760463 PMCID: PMC9903906 DOI: 10.3114/sim.2022.102.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/03/2022] [Indexed: 01/09/2023] Open
Abstract
Aspergillus section Candidi encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, food, feed, clinical material, soil and dung. Their identification is non-trivial due to largely uniform morphology. This study aims to re-evaluate the species boundaries in the section Candidi and present an overview of all existing species along with information on their ecology. For the analyses, we assembled a set of 113 strains with diverse origin. For the molecular analyses, we used DNA sequences of three house-keeping genes (benA, CaM and RPB2) and employed species delimitation methods based on a multispecies coalescent model. Classical phylogenetic methods and genealogical concordance phylogenetic species recognition (GCPSR) approaches were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth at temperatures ranging from 10 to 45 °C. Based on the integrative approach comprising four criteria (phylogenetic and phenotypic), all currently accepted species gained support, while two new species are proposed (A. magnus and A. tenebricus). In addition, we proposed the new name A. neotritici to replace an invalidly described A. tritici. The revised section Candidi now encompasses nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (e.g., A. subalbidus and A. campestris) while others are more uniform (e.g., A. candidus or A. pragensis). The growth rates on different media and at different temperatures, colony colours, production of soluble pigments, stipe dimensions and vesicle diameters contributed the most to the phenotypic species differentiation. Taxonomic novelties: New species: Aspergillus magnus Glässnerová & Hubka; Aspergillus neotritici Glässnerová & Hubka; Aspergillus tenebricus Houbraken, Glässnerová & Hubka. Citation: Glässnerová K, Sklenář F, Jurjević Ž, Houbraken J, Yaguchi T, Visagie CM, Gené J, Siqueira JPZ, Kubátová A, Kolařík M, Hubka V (2022). A monograph of Aspergillus section Candidi. Studies in Mycology 102: 1-51. doi: 10.3114/sim.2022.102.01.
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Affiliation(s)
- K. Glässnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Ž. Jurjević
- EMSL Analytical, Cinnaminson, New Jersey, USA
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J.P.Z. Siqueira
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Laboratório de Microbiologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - A. Kubátová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - M. Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
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Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). Front Plant Sci 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
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Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
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Allman ES, Mitchell JD, Rhodes JA. Gene tree discord, simplex plots, and statistical tests under the coalescent. Syst Biol 2021; 71:929-942. [PMID: 33560348 DOI: 10.1093/sysbio/syab008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.
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Affiliation(s)
- Elizabeth S Allman
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA
| | - Jonathan D Mitchell
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA.,Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - John A Rhodes
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA
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Sklenář F, Jurjević Ž, Peterson SW, Kolařík M, Nováková A, Flieger M, Stodůlková E, Kubátová A, Hubka V. Increasing the species diversity in the Aspergillus section Nidulantes: Six novel species mainly from the indoor environment. Mycologia 2020; 112:342-370. [PMID: 32074019 DOI: 10.1080/00275514.2019.1698923] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aspergillus section Nidulantes encompasses almost 80 homothallic and anamorphic species, mostly isolated from soil, plant material, or the indoor environment. Some species are clinically relevant or produce mycotoxins. This study reevaluated the species boundaries within several clades of section Nidulantes. Five data sets were assembled, each containing presumptive new species and their closest relatives, and phylogenetic and phenotypic analyses were performed. We tested the hypotheses that the newly isolated or reexamined strains constitute separate species (splitting approach) or should be treated as part of broadly defined species (lumping approach). Four DNA sequence loci were amplified, internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA and partial sequences of the β-tubulin (benA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) genes. The latter three loci were used for the phylogenetic analysis and served as input for single-locus (GMYC, bGMYC, PTP, and bPTP) and multilocus (STACEY and BP&P) species delimitation analyses. The phenotypic analysis comprised macro- and micromorphology (including scanning electron microscopy) and comparison of cardinal growth temperatures. The phylogenetic analysis supported the splitting hypothesis in all cases, and based on the combined approach, we propose six new species, four that are homothallic and two anamorphic. Four new species were isolated from the indoor environment (Jamaica, Trinidad and Tobago, USA), one originated from soil (Australia), and one from a kangaroo rat cheek pouch (USA).
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Affiliation(s)
- F Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - Ž Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, New Jersey 08077
| | - S W Peterson
- US Department of Agriculture, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, Illinois 61604
| | - M Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - A Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - M Flieger
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - E Stodůlková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - A Kubátová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - V Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
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Sklenář F, Jurjević Ž, Zalar P, Frisvad JC, Visagie CM, Kolařík M, Houbraken J, Chen AJ, Yilmaz N, Seifert KA, Coton M, Déniel F, Gunde-Cimerman N, Samson RA, Peterson SW, Hubka V. Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti. Stud Mycol 2017; 88:161-236. [PMID: 29158611 DOI: 10.1016/j.simyco.2017.09.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
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Key Words
- Aspergillus canadensis Visagie, Yilmaz, F. Sklenar & Seifert
- Aspergillus clavatophorus F. Sklenar, S.W. Peterson & Hubka
- Aspergillus destruens Zalar, F. Sklenar, S.W. Peterson & Hubka
- Aspergillus domesticus F. Sklenar, Houbraken, Zalar & Hubka
- Aspergillus glabripes F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus hordei F. Sklenar, S.W. Peterson & Hubka
- Aspergillus infrequens F. Sklenar, S.W. Peterson & Hubka
- Aspergillus magnivesiculatus F. Sklenar, Zalar, Ž. Jurjević & Hubka
- Aspergillus pachycaulis F. Sklenar, S.W. Peterson, Ž. Jurjević & Hubka
- Aspergillus penicillioides
- Aspergillus pseudogracilis F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus restrictus
- Aspergillus reticulatus F. Sklenar, Ž. Jurjević, S.W. Peterson & Hubka
- Aspergillus salinicola Zalar, F. Sklenar, Visagie & Hubka
- Aspergillus tardicrescens F. Sklenar, Houbraken, Zalar, & Hubka
- Aspergillus villosus F. Sklenar, S.W. Peterson & Hubka
- Eurotium
- food spoilage
- indoor fungi
- linear discriminant analysis
- multigene phylogeny
- multispecies coalescent model
- sick building syndrome
- xerophilic fungi
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