1
|
Haug I, Setaro S, Suárez JP. Species composition of arbuscular mycorrhizal communities changes with elevation in the Andes of South Ecuador. PLoS One 2019; 14:e0221091. [PMID: 31419262 PMCID: PMC6697372 DOI: 10.1371/journal.pone.0221091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/30/2019] [Indexed: 12/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are the most prominent mycobionts of plants in the tropics, yet little is known about their diversity, species compositions and factors driving AMF distribution patterns. To investigate whether elevation and associated vegetation type affect species composition, we sampled 646 mycorrhizal samples in locations between 1000 and 4000 m above sea level (masl) in the South of Ecuador. We estimated diversity, distribution and species compositions of AMF by cloning and Sanger sequencing the 18S rDNA (the section between AML1 and AML2) and subsequent derivation of fungal OTUs based on 99% sequence similarity. In addition, we analyzed the phylogenetic structure of the sites by computing the mean pairwise distance (MPD) and the mean nearest taxon difference (MNTD) for each elevation level. It revealed that AMF species compositions at 1000 and 2000 masl differ from 3000 and 4000 masl. Lower elevations (1000 and 2000 masl) were dominated by members of Glomeraceae, whereas Acaulosporaceae were more abundant in higher elevations (3000 and 4000 masl). Ordination of OTUs with respect to study sites revealed a correlation to elevation with a continuous turnover of species from lower to higher elevations. Most of the abundant OTUs are not endemic to South Ecuador. We also found a high proportion of rare OTUs at all elevations: 79-85% of OTUs occurred in less than 5% of the samples. Phylogenetic community analysis indicated clustering and evenness for most elevation levels indicating that both, stochastic processes and habitat filtering are driving factors of AMF community compositions.
Collapse
Affiliation(s)
- Ingeborg Haug
- Evolutionary Ecology of Plants, Eberhard-Karls-University, Tübingen, Germany
| | - Sabrina Setaro
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| |
Collapse
|
2
|
Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182. [PMID: 31097708 PMCID: PMC6522516 DOI: 10.1038/s41467-019-10210-3] [Citation(s) in RCA: 1509] [Impact Index Per Article: 301.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
Collapse
Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| |
Collapse
|
3
|
Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages. Sci Rep 2018; 8:2539. [PMID: 29416071 PMCID: PMC5803224 DOI: 10.1038/s41598-018-20833-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009–2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 µm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.
Collapse
|
4
|
Zielezinski A, Vinga S, Almeida J, Karlowski WM. Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol 2017; 18:186. [PMID: 28974235 PMCID: PMC5627421 DOI: 10.1186/s13059-017-1319-7] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
Collapse
Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Susana Vinga
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
| | - Jonas Almeida
- Stony Brook University (SUNY), 101 Nicolls Road, Stony Brook, NY, 11794, USA
| | - Wojciech M Karlowski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
| |
Collapse
|
5
|
Morard R, Escarguel G, Weiner AKM, André A, Douady CJ, Wade CM, Darling KF, Ujiié Y, Seears HA, Quillévéré F, de Garidel-Thoron T, de Vargas C, Kucera M. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Syst Biol 2016; 65:925-40. [PMID: 27073250 DOI: 10.1093/sysbio/syw031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
Collapse
Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
| | - Gilles Escarguel
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Agnes K M Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan
| | - Aurore André
- Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France
| | - Christophe J Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Christopher M Wade
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK, School of Geography and GeoSciences, University of St Andrews, Fife KY16 9AL, UK
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Heidi A Seears
- Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA
| | - Frédéric Quillévéré
- Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Thibault de Garidel-Thoron
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
| |
Collapse
|
6
|
Garnica S, Riess K, Schön ME, Oberwinkler F, Setaro SD. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage. PLoS One 2016; 11:e0149531. [PMID: 26938104 PMCID: PMC4795679 DOI: 10.1371/journal.pone.0149531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/02/2016] [Indexed: 01/03/2023] Open
Abstract
Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales.
Collapse
Affiliation(s)
- Sigisfredo Garnica
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Kai Riess
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Max E. Schön
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Franz Oberwinkler
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Sabrina D. Setaro
- Wake Forest University, Department of Biology, 205 Winston Hall, 1834 Wake Forest Road, Winston-Salem, North Carolina, 27106, United States of America
| |
Collapse
|
7
|
Wang QM, Yurkov A, Göker M, Lumbsch H, Leavitt S, Groenewald M, Theelen B, Liu XZ, Boekhout T, Bai FY. Phylogenetic classification of yeasts and related taxa within Pucciniomycotina. Stud Mycol 2016; 81:149-89. [PMID: 26951631 PMCID: PMC4777780 DOI: 10.1016/j.simyco.2015.12.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.
Collapse
Key Words
- B. aurantiaca (Saito) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. kluyveri-nielii (van der Walt) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. ogasawarensis (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. phyllomatis (van der Walt & Y. Yamada) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. salicina (B.N. Johri & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. syzygii (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. taupoensis (Hamam. & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- B. yamatoana (Nakase, M. Suzuki & M. Itoh) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ballistosporomycessasicola (Nakase & M. Suzuki) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Bannoabischofiae (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozymaarctica (Vishniac & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaarmeniaca (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. diffluens (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. eucalyptica (C.H. Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. falcata (Nakase, M. Itoh & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. foliorum (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. griseoflava (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. lophatheri (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. philyla (van der Walt, Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. retinophila (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. terpenoidalis (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymafushanensis (Nakase, F.L. Lee & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeacycloclastica (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiopsislactophilus (Nakase, M. Itoh, M. Suzuki & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiumportillonense (F. Laich, I. Vaca & R. Chávez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- E. yunnanense (F.Y. Bai, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Erythrobasidiumelongatum (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozymainositophila (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fungi
- GMYC approach
- H. singularis (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoa Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoalignophila (Dill, C. Ramírez & González) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazymalactosa (Hasegawa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyunia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyuniasakaguchii (Sugita, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- K. miscanthi (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. phyllada (van der Walt & Y. Yamada) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. sorbi (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. subrosea (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. thailandica (Fungsin, Hamam. & Nakase ) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. yuccicola (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- Kondoachangbaiensis (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- M. magnisporus (Nakase, Tsuzuki, F.L. Lee, Sugita, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. orientis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. pini (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycesbloemfonteinensis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycetaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Molecular phylogeny
- O. straminea (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- O. yarrowii (Á. Fonseca & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozymasilvestris (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. buffonii (C. Ramírez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. corallina (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. dimennae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. glacialis (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. himalayensis (Shivaji, Bhadra & Rao) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. linderae (Nakase, M. Takash. & Hamam.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. musae (M. Takash., S.O. Suh & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- P. novozealandica (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. producta (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. psychrophila (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. pustula (Buhagiar) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. subbrunnea (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferiapsychrophenolica (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozymacoprosmicola (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phylogenetic rank boundary optimisation
- Pseudobensingtonia F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudobensingtoniaingoldii (Nakase & Itoh.) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudohyphozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pseudohyphozymabogoriensis (Deinema) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pucciniomycotina
- R. azoricus (J.P. Samp. & Gadanho) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. babjevae (Golubev) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. colostri (T. Castelli) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diobovata (S.Y. Newell & I.L. Hunter) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diospyroris (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. dracophylli (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. kratochvilovae (Hamam., Sugiy. & Komag.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. lusitaniae (Á. Fonseca & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. microsporus (Higham ex Fell, Blatt & Statzell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. nylandii (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. odoratus (J.P. Samp., Á. Fonseca & Valério) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. paludigena (Fell & Tallman) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. poonsookiae (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. pyrrosiae (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. rubra (Nakase, Oakada & Sugiy.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. ruineniae (Holzschu, Tredick & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. sphaerocarpa (S.Y. Newell & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. toruloides (I. Banno) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus fluvialis (Fell, Kurtzman, Tallman & J.D. Buck) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodotorulaalborubescens (Derx) Q.M. Wang, F.Y. Bai, Groenew. & Boekhout
- Ruinenia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaclavata (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. oryzae (F.Y. Bai & Y.M. Cai) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. foliicola (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. gracilis (Derx) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. johnsonii (Nyland) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. lamellibrachiae (Nagah., Hamam., Nakase & Horikoshi) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. marina (Phaff, Mrak & Williams) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. meli (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. novozelandica (W.B. Kendr. & X.D. Gong) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. pilati (F.H. Jacob, Faure-Raynaud & Berton) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. pulcherrima (J.E. Wright) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. symmetrica (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. tsugae (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vanillica (J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vermiculata (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiacladiensis (Fell, Statzell & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozymaingeniosa (Di Menna) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia cresolica (Middelhoven & Spaaij) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozymacrocea (Shifrine & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spiculogloeomycetes Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sporobolomyceslongiusculus (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sterigmatomyceshyphaenes (Har. & Pat.) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- Symmetrospora Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporacoprosmae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Taxonomy
- Trigonosporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Trigonosporomyceshylophilus (van der Walt, van der Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozymaferulica (J.P. Samp. & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ustilentylomagraminis (Rodr. Mir. & Diem) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxula Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxulajavanica (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Y. sonckii (Hopsu-Havu, Tunnela & Yarrow) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamycesrosulatus (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yeasts
- Yunzhangia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yunzhangiaauriculariae (Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
Collapse
Affiliation(s)
- Q.-M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - A.M. Yurkov
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - M. Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - H.T. Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - S.D. Leavitt
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - M. Groenewald
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Theelen
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - X.-Z. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - T. Boekhout
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Correspondence: T. Boekhout; F.-Y. Bai
| | - F.-Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence: T. Boekhout; F.-Y. Bai
| |
Collapse
|
8
|
Liu XZ, Wang QM, Göker M, Groenewald M, Kachalkin A, Lumbsch H, Millanes A, Wedin M, Yurkov A, Boekhout T, Bai FY. Towards an integrated phylogenetic classification of the Tremellomycetes. Stud Mycol 2015; 81:85-147. [PMID: 26955199 PMCID: PMC4777781 DOI: 10.1016/j.simyco.2015.12.001] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.
Collapse
Key Words
- A. cacaoliposimilis (J.L. Zhou, S.O. Suh & Gujjari) Kachalkin, A.M. Yurkov & Boekhout
- A. dehoogii (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. domesticum (Sugita, A. Nishikawa & Shinoda) A.M. Yurkov & Boekhout
- A. dulcitum (Berkhout) A.M. Yurkov & Boekhout
- A. gamsii (Middelhoven, Scorzetti, Sigler & Fell) A.M. Yurkov & Boekhout
- A. gracile (Weigmann & A. Wolff) A.M. Yurkov & Boekhout
- A. laibachii (Windisch) A.M. Yurkov & Boekhout
- A. lignicola (Diddens) A.M. Yurkov & Boekhout
- A. loubieri (Morenz) A.M. Yurkov & Boekhout
- A. montevideense (L.A. Queiroz) A.M. Yurkov & Boekhout
- A. mycotoxinivorans (O. Molnár, Schatzm. & Prillinger) A.M. Yurkov & Boekhout
- A. scarabaeorum (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. siamense (Nakase, Jindam., Sugita & H. Kawas.) Kachalkin, A.M. Yurkov & Boekhout
- A. sporotrichoides (van Oorschot) A.M. Yurkov & Boekhout
- A. vadense (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. veenhuisii (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. wieringae (Middelhoven) A.M. Yurkov & Boekhout
- A. xylopini (S.O. Suh, Lee, Gujjari & Zhou) Kachalkin, A.M. Yurkov & Boekhout
- Apiotrichumbrassicae (Nakase) A.M. Yurkov & Boekhout
- Bandonia A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bandoniamarina (van Uden & Zobell) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. foliicola (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. hainanense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. panici (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. pseudovariabile (F.Y. Bai, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. sanyaense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. setariae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. siamense (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. variabile (Nakase & M. Suzuki) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. wuzhishanense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleraceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidiaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidiumbegoniae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Carc. polyporina (D.A. Reid) A.M. Yurkov
- Carcinomycesarundinariae (Fungsin, M. Takash. & Nakase) A.M. Yurkov
- Carlosrosaea A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Carlosrosaeavrieseae (Landell, Brandão, Safar, Gomes, Félix, Santos, Pagani, Ramos, Broetto, Mott, Valente & Rosa) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cr. luteus (Roberts) Boekhout, Liu, Bai & M. Groenew.
- Cryptococcusdepauperatus (Petch) Boekhout, Liu, Bai & M. Groenew.
- Cu. curvatus (Diddens & Lodder) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. cutaneum (de Beurmann, Gougerot & Vaucher) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. cyanovorans (Motaung, Albertyn, J.L.F. Kock et Pohl) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. daszewskae (Takash., Sugita, Shinoda & Nakase) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. debeurmannianum (Sugita, Takash., Nakase & Shinoda) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. dermatis (Sugita, Takash., Nakase, Ichikawa, Ikeda & Shinoda) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. guehoae (Middelhoven, Scorzettii & Fell) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. haglerorum (Middelhoven, Á. Fonseca, S.C. Carreiro, Pagnocca & O.C. Bueno) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. jirovecii (Frágner) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. moniliiforme (Weigmann & A. Wolff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. mucoides (E. Guého & M.T. Smith) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. oleaginosus (J.J. Zhou, S.O. Suh & Gujjari) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. smithiae (Middelhoven, Scorzetti, Sugita & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. terricola (Sugita, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cutaneotrichosporon X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cutaneotrichosporonarboriformis (Sugita, M. Takash., Sano, Nishim., Kinebuchi, S. Yamag. & Osanai) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Dimennazyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Dimennazyma cistialbidi (Á. Fonseca, J. Inácio & Spenc.-Mart.) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Effuseotrichosporon A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Effuseotrichosporon vanderwaltii (Motaung, Albertyn, Kock, C.F. Lee, S.O. Suh, M. Blackwell & C.H. Pohl) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. magnum (Lodder & Kreger-van Rij) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. oeirense (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. stepposum (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. wieringae (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Filobasidium chernovii (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fon. mujuensis (K.S. Shin & Y.H. Park) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fon. tronadorensis (V. De Garcia, Zalar, Brizzio, Gunde-Cim. & van Brook) A.M. Yurkov
- Fonsecazyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fonsecazyma betulae (K. Sylvester, Q.M. Wang, C. T. Hittinger) A.M. Yurkov, A.V. Kachalkin & Boekhout
- Gelidatrema A.M. Yurkov, X.Z. Liu, F.Y. Bai
- Gelidatrema spencermartinsiae (Garcia, Brizzio, Boekhout, Theelen, Libkind & van Broock) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. armeniaca (Á. Fonseca & J. Inácio) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. bromeliarum (Landell & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. tibetensis (F.Y. Bai & Q.M. Wang) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria amylolytica (Á. Fonseca, J. Inácio & Spenc.-Mart.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. agrionensis (Russo, Libkind, Samp. & van Broock) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. gastrica (Reiersöl & di Menna) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. gilvescens (Chernov & Babeva) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. iberica (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. metallitolerans (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Goffeauzyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Goffeauzyma aciditolerans (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Haglerozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Haglerozymachiarellii (Pagnocca, Legaspe, Rodrigues & Ruivo) A. M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Het. bachmannii (Diederich & M.S. Christ.) Millanes & Wedin
- Het. physciacearum (Diederich) Millanes & Wedin
- Heterocephalacriaarrabidensis (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Itersoniliapannonica (Niwata, Takash., Tornai-Lehoczki, T. Deák & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Jelly fungi
- Ko. distylii (Hamam., Kuroy. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. fuzhouensis (J.Z. Yue) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. lichenicola (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai
- Ko. mexicana (Lopandic, O. Molnár & Prillinger) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. ogasawarensis (Hamam., Kuroy. & Nakase) X.Z. Liu, F.Y. Bai, Groenew. & Boekhout
- Ko. sichuanensis (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaellachinensis (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaellaprillingeri (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kr. tahquamenonensis (Wang, Hulfachor, Sylvester and Hittinger) A.M. Yurkov
- Krasilnikovozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Krasilnikovozymahuempii (C. Ramírez & A. E. González) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. dejecticola (Thanh, Hai & Lachance) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. dendrophila (Van der Walt & D.B. Scott) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. pini (Golubev & Pfeiffer) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. shivajii (S.R. Ravella, S.A. James, C.J. Bond, I.N. Roberts, K. Cross, Retter & P.J. Hobbs) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kwoniellabestiolae (Thanh, Hai & Lachance) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- M. Groenew. & Boekhout
- M. cryoconiti (Margesin & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- M. niccombsii (Thomas-Hall) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Morphology
- Mrakiaaquatica (E.B.G. Jones & Slooff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Mrakiaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Multigene phylogeny
- Naem. microspora (Lloyd) Millanes & Wedin
- Naemateliaaurantialba (Bandoni & M. Zang) Millanes & Wedin
- Naemateliaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. albida (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. albidosimilis (Vishniac & Kurtzman) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. antarctica (Vishniac & Kurtzman) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. bhutanensis (Goto & Sugiy.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. cerealis (Passoth, A.-C. Andersson, Olstorpe, Theelen, Boekhout & Schnürer) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. diffluens (Zach) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. friedmannii (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. liquefaciens (Saito & M. Ota) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. onofrii (Turchetti, Selbmann & Zucconi) A.M. Yurkov
- Nag. randhawae (Z.U. Khan, S.O. Suh. Ahmad, F. Hagen, Fell, Kowshik, Chandy & Boekhout) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. uzbekistanensis (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. vaughanmartiniae (Turchetti, Blanchette & Arenz) A.M. Yurkov
- Nag. vishniacii (Vishniac & Hempfling) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Naganishiaadeliensis (Scorzetti, I. Petrescu, Yarrow & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Niel. melastomae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozymaformosana (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- P. mycophaga (G.W. Martin) Millanes & Wedin
- Pap. aspenensis (K. Ferreira-Paim, T.B. Ferreira, L. Andrade-Silva, D.J. Mora, D.J. Springer, J. Heitman, F.M. Fonseca, D. Matos, M.S.C. Melhem & M.L. Silva-Vergara) X.Z. Liu, F.Y. Bai, A.M. Yurkov & Boekhout
- Pap. aurea (Saito) M. Takash., Sugita, Shinoda & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. baii (A.M. Yurkov, M.A. Guerreiro & Á. Fonseca) A.M. Yurkov
- Pap. flavescens (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. fonsecae (V. de García, Zalar, Braizzio, Gunde-Cim. & van Brollck) A.M. Yurkov
- Pap. frias (V. de García, Zalar, Braizzio, Gunde-Cim. & van Brollck) A.M. Yurkov
- Pap. fuscus (J.P. Samp., J. Inácio, Fonseca & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. hoabinhensis (D.T. Luong, M. Takash., Ty. Dung & Nakase) A.M. Yurkov
- Pap. japonica (J.P. Samp., Fonseca & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. laurentii (Kuff.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. mangalensis (Fell, Statzell & Scorzett) A.M. Yurkov
- Pap. nemorosus (Golubev, Gadanho, J.P. Samp. & N.W. Golubev) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. perniciosus (Golubev, Gadanho, J.P. Samp. & N.W. Golubev) X.Z. Liu, F.Y. Bai
- Pap. pseudoalba (Nakase & M. Suzuki) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. rajasthanensis (Saluja & G.S. Prasad) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. ruineniae (A.M. Yurkov, M.A. Guerreiro & Á. Fonseca) A.M. Yurkov
- Pap. taeanensis (K.S. Shin & Y.H. Park) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. terrestris (Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. wisconsinensis (Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotremaanemochoreius (C.H. Pohl, Kock, P.W.J. van Wyk & Albertyn) F.Y. Bai, M. Groenew. & Boekhout
- Ph. mycetophiloides (Kobayasi) Millanes & Wedin
- Ph. neofoliacea (Chee J. Chen) Millanes & Wedin
- Ph. simplex (H.S. Jacks. & G.W. Martin) Millanes & Wedin
- Ph. skinneri (Phaff & Carmo Souza) A.M. Yurkov & Boekhout
- Phaeotremellaceae A.M. Yurkov & Boekhout
- Phaeotremellafagi (Middelhoven & Scorzetti) A.M. Yurkov & Boekhout
- Pis. cylindrica (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pis. fildesensis (T. Zhang & L.-Y. Yu) A.M. Yurkov
- Pis. filicatus (Golubev & J.P. Samp.) Kachalkin
- Pis. silvicola (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, Groenew. & Boekhout
- Pis. sorana (Hauerslev) A.M. Yurkov
- Pis. taiwanensis (Nakase, Tsuzuki & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Piskurozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Piskurozymacapsuligena (Fell, Statzell, I.L. Hunter & Phaff) A.M. Yurkov
- Piskurozymaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ps. lacticolor (Satoh & Makimura) A.M. Yurkov
- Ps. moriformis (Berk.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ps. nivalis (Chee J. Chen) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pseudotremella X.Z. Liu, F.Y. Bai, A.M. Yurkov, M. Groenew. & Boekhout
- Pseudotremellaallantoinivorans (Middelhoven) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- R. complexa (Landell, Pagnocca, Sette, Passarini, Garcia, Ribeiro, Lee, Brandao, Rosa & Valente) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. fermentans (Lee) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. glucofermentans (S.O. Suh & Blackwell) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. nanyangensis (F.L. Hui & Q.H. Niu) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. noutii (Boekhout, Fell, Scorzett & Theelen) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. tunnelae (Boekhout, Fell, Scorzetti & Theelen) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. visegradensis (Peter & Dlauchy) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Ranks
- Rhynchogastremaaquatica (Brandao, Valente, Pimenta & Rosa) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Sait. ninhbinhensis (Luong, Takash., Dung & Nakase) A.M. Yurkov
- Sait. paraflava (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sait. podzolica (Babeva & Reshetova) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Saitozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Saitozymaflava (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sol. fuscescens (Golubev) A.M. Yurkov
- Sol. keelungensis (C.F. Chang & S.M. Liu) A.M. Yurkov
- Sol. phenolicus (Á. Fonseca, Scorzetti & Fell) A.M. Yurkov
- Sol. terreus (Di Menna) A.M. Yurkov
- Sol. terricola (T.A. Pedersen) A.M. Yurkov
- Solicoccozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Solicoccozymaaeria (Saito) A.M. Yurkov
- Sugitazyma A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sugitazymamiyagiana (Nakase, Itoh, Takem. & Bandoni) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Tausoniapullulans (Lindner) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Taxonomy
- Tremellayokohamensis (Alshahni, Satoh & Makimura) A.M. Yurkov
- Tremellomycetes
- Trimorphomycessakaeraticus (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Trimorphomycetaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Van. meifongana (C.F. Lee) Kachalkin, A.M. Yurkov & Boekhout
- Van. nantouana (C.F. Lee) Kachalkin, A.M. Yurkov & Boekhout
- Van. thermophila (Vogelmann, Chaves & Hertel) Kachalkin, A.M. Yurkov & Boekhout
- Vanrijafragicola (M. Takash., Sugita, Shinoda & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. dimennae (Fell & Phaff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. foliicola (Q.M. Wang & F.Y. Bai) A.M. Yurkov
- Vis. globispora (B.N. Johri & Bandoni) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. heimaeyensis (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. nebularis (Vishniac) A.M. Yurkov
- Vis. peneaus (Phaff, Mrak & O.B. Williams) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. psychrotolerans (V. de García, Zalar, Brizzio, Gunde-Cim. & van Broock) A.M. Yurkov
- Vis. taibaiensis (Q.M. Wang & F.Y. Bai) A.M. Yurkov
- Vis. tephrensis (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. victoriae (M.J. Montes, Belloch, Galiana, M.D. García, C. Andrés, S. Ferrer, Torr.-Rodr. & J. Guinea) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozymacarnescens (Verona & Luchetti) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Yeasts
Collapse
Affiliation(s)
- X.-Z. Liu
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - Q.-M. Wang
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - M. Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - M. Groenewald
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - A.V. Kachalkin
- Faculty of Soil Science, Lomonosov Moscow State University, Moscow 119991, Russia
| | - H.T. Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - A.M. Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain
| | - M. Wedin
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden
| | - A.M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - T. Boekhout
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - F.-Y. Bai
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| |
Collapse
|
9
|
Flynn JM, Brown EA, Chain FJJ, MacIsaac HJ, Cristescu ME. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol Evol 2015; 5:2252-66. [PMID: 26078860 PMCID: PMC4461425 DOI: 10.1002/ece3.1497] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 11/05/2022] Open
Abstract
Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive.
Collapse
Affiliation(s)
- Jullien M Flynn
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
| | - Emily A Brown
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1 ; Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada
| | - Frédéric J J Chain
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
| | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
| |
Collapse
|
10
|
Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B. Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Mol Ecol Resour 2014; 15:526-42. [PMID: 25270047 DOI: 10.1111/1755-0998.12336] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 09/20/2014] [Accepted: 09/24/2014] [Indexed: 01/26/2023]
Abstract
Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.
Collapse
Affiliation(s)
- Jonas Zimmermann
- Justus-Liebig-University Giessen, AG Spezielle Botanik, Heinrich-Buff-Ring 38, 35392, Giessen, Germany; Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
| | | | | | | | | |
Collapse
|
11
|
André A, Quillévéré F, Morard R, Ujiié Y, Escarguel G, de Vargas C, de Garidel-Thoron T, Douady CJ. SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications. PLoS One 2014; 9:e104641. [PMID: 25119900 PMCID: PMC4131912 DOI: 10.1371/journal.pone.0104641] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/11/2014] [Indexed: 11/21/2022] Open
Abstract
The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.
Collapse
Affiliation(s)
- Aurore André
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 6112: Laboratoire de Planétologie et de Géodynamique - Bioindicateurs Actuels et Fossiles, Université d'Angers, Angers, France
| | - Frédéric Quillévéré
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France
| | - Raphaël Morard
- Zentrum für marine Umweltwissenschaften MARUM, Universität Bremen, Bremen, Germany
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Matsumoto, Japan
| | - Gilles Escarguel
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144: Evolution des Protistes et des Ecosystèmes Pélagiques, Université Pierre et Marie Curie-Station Biologique de Roscoff, Roscoff, France
| | - Thibault de Garidel-Thoron
- Centre National de la Recherche Scientifique, Centre de Recherche et d'Enseignement de Géosciences de l'Environnement, Université Aix-Marseille, Aix-en-Provence, France
| | - Christophe J. Douady
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5023: Ecologie des Hydrosystèmes Fluviaux, Université Lyon 1, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| |
Collapse
|
12
|
Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units. Fungal Biol 2014; 118:559-78. [DOI: 10.1016/j.funbio.2013.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 11/18/2022]
|
13
|
Weiner AKM, Weinkauf MFG, Kurasawa A, Darling KF, Kucera M, Grimm GW. Phylogeography of the tropical planktonic foraminifera lineage globigerinella reveals isolation inconsistent with passive dispersal by ocean currents. PLoS One 2014; 9:e92148. [PMID: 24663038 PMCID: PMC3963880 DOI: 10.1371/journal.pone.0092148] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/17/2014] [Indexed: 11/18/2022] Open
Abstract
Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates.
Collapse
Affiliation(s)
- Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- * E-mail:
| | - Manuel F. G. Weinkauf
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Atsushi Kurasawa
- Institute of Biogeosciences, Japanese Agency for Marine Earth Science and Technology, Yokosuka, Japan
| | - Kate F. Darling
- School of Geosciences and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Guido W. Grimm
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| |
Collapse
|
14
|
Ezard THG, Thomas GH, Purvis A. Inclusion of a near-complete fossil record reveals speciation-related molecular evolution. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12089] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Thomas H. G. Ezard
- Centre for Biological Sciences; University of Southampton; Life Sciences Building 85, Highfield Campus; Southampton; SO17 1BJ; UK
| | - Gavin H. Thomas
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield; S10 2TN; UK
| | - Andy Purvis
- Department of Life Sciences; Imperial College London; Silwood Park Campus; Ascot; Berkshire; SL5 7PY; UK
| |
Collapse
|
15
|
Miralles A, Vences M. New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One 2013; 8:e68242. [PMID: 23874561 PMCID: PMC3710018 DOI: 10.1371/journal.pone.0068242] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/24/2013] [Indexed: 01/17/2023] Open
Abstract
Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.
Collapse
Affiliation(s)
- Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
| | | |
Collapse
|
16
|
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60. [PMID: 23432962 PMCID: PMC3665452 DOI: 10.1186/1471-2105-14-60] [Citation(s) in RCA: 4680] [Impact Index Per Article: 425.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept. RESULTS Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions. CONCLUSIONS Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.
Collapse
Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
17
|
Garnica S, Riess K, Bauer R, Oberwinkler F, Weiß M. Phylogenetic diversity and structure of sebacinoid fungi associated with plant communities along an altitudinal gradient. FEMS Microbiol Ecol 2012; 83:265-78. [DOI: 10.1111/j.1574-6941.2012.01473.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sigisfredo Garnica
- Chair of Plant Evolutionary Ecology; Institute of Evolution and Ecology; University of Tübingen; Tübingen; Germany
| | - Kai Riess
- Chair of Plant Evolutionary Ecology; Institute of Evolution and Ecology; University of Tübingen; Tübingen; Germany
| | - Robert Bauer
- Chair of Plant Evolutionary Ecology; Institute of Evolution and Ecology; University of Tübingen; Tübingen; Germany
| | - Franz Oberwinkler
- Chair of Plant Evolutionary Ecology; Institute of Evolution and Ecology; University of Tübingen; Tübingen; Germany
| | - Michael Weiß
- Chair of Plant Evolutionary Ecology; Institute of Evolution and Ecology; University of Tübingen; Tübingen; Germany
| |
Collapse
|
18
|
Weiner A, Aurahs R, Kurasawa A, Kitazato H, Kucera M. Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist. Mol Ecol 2012; 21:4063-73. [PMID: 22738662 DOI: 10.1111/j.1365-294x.2012.05686.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A large portion of the surface-ocean biomass is represented by microscopic unicellular plankton. These organisms are functionally and morphologically diverse, but it remains unclear how their diversity is generated. Species of marine microplankton are widely distributed because of passive transport and lack of barriers in the ocean. How does speciation occur in a system with a seemingly unlimited dispersal potential? Recent studies using planktonic foraminifera as a model showed that even among the cryptic genetic diversity within morphological species, many genetic types are cosmopolitan, lending limited support for speciation by geographical isolation. Here we show that the current two-dimensional view on the biogeography and potential speciation mechanisms in the microplankton may be misleading. By depth-stratified sampling, we present evidence that sibling genetic types in a cosmopolitan species of marine microplankton, the planktonic foraminifer Hastigerina pelagica, are consistently separated by depth throughout their global range. Such strong separation between genetically closely related and morphologically inseparable genetic types indicates that niche partitioning in marine heterotrophic microplankton can be maintained in the vertical dimension on a global scale. These observations indicate that speciation along depth (depth-parapatric speciation) can occur in vertically structured microplankton populations, facilitating diversification without the need for spatial isolation.
Collapse
Affiliation(s)
- Agnes Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany.
| | | | | | | | | |
Collapse
|
19
|
Boykin LM, Armstrong KF, Kubatko L, De Barro P. Species delimitation and global biosecurity. Evol Bioinform Online 2011; 8:1-37. [PMID: 22267902 PMCID: PMC3256992 DOI: 10.4137/ebo.s8532] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification.
Collapse
Affiliation(s)
- Laura M Boykin
- Bio-Protection Research Centre, PO Box 84, Lincoln University, Lincoln 7647, New Zealand
| | | | | | | |
Collapse
|
20
|
Genea mexicana, sp. nov., and Geopora tolucana, sp. nov., new hypogeous Pyronemataceae from Mexico, and the taxonomy of Geopora reevaluated. Mycol Prog 2011. [DOI: 10.1007/s11557-011-0781-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
21
|
Aze T, Ezard THG, Purvis A, Coxall HK, Stewart DRM, Wade BS, Pearson PN. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol Rev Camb Philos Soc 2011; 86:900-27. [DOI: 10.1111/j.1469-185x.2011.00178.x] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
22
|
Stielow B, Bratek Z, Orczán AKI, Rudnoy S, Hensel G, Hoffmann P, Klenk HP, Göker M. Species delimitation in taxonomically difficult fungi: the case of Hymenogaster. PLoS One 2011; 6:e15614. [PMID: 21311589 PMCID: PMC3027480 DOI: 10.1371/journal.pone.0015614] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 11/17/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions. METHODOLOGY In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software. CONCLUSIONS Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19(th) century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general.
Collapse
Affiliation(s)
- Benjamin Stielow
- DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Zoltan Bratek
- Department of Plant Physiology and Molecular Plant Biology, ELTE University, Budapest, Hungary
| | - Akos Kund I. Orczán
- Department of Plant Physiology and Molecular Plant Biology, ELTE University, Budapest, Hungary
| | - Szabolcs Rudnoy
- Department of Plant Physiology and Molecular Plant Biology, ELTE University, Budapest, Hungary
| | | | - Peter Hoffmann
- DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|