A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences
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Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Alverson, 2007, Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms, Mol. Phylogenet. Evol., 45, 193, 10.1016/j.ympev.2007.03.024
Berger, 2011, Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood, Syst. Biol., 60, 291, 10.1093/sysbio/syr010
Enquist, 2002, General patterns of taxonomic and biomass partitioning in extant and fossil plant communities, Nature, 419, 610, 10.1038/nature01069
Feau, 2011, Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model Fungi, PLoS ONE, 6
Federhen, 2012, The NCBI taxonomy database, Nucleic Acids Res., 40, D136, 10.1093/nar/gkr1178
Forest, 2007, Preserving the evolutionary potential of floras in biodiversity hotspots, Nature, 445, 757, 10.1038/nature05587
Ghikas, 2010, Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii, BMC Microbiol., 10, 10.1186/1471-2180-10-174
Gryganskyi, 2013, Phylogenetic lineages in Entomophthoromycota, Persoonia, 30, 94, 10.3767/003158513X666330
Hamady, 2010, Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data, ISME J., 4, 17, 10.1038/ismej.2009.97
Hawksworth, 2012, Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate?, Biodivers. Conserv., 21, 2425, 10.1007/s10531-012-0335-x
Hinchliff, 2015, Synthesis of phylogeny and taxonomy into a comprehensive tree of life, Proc. Natl. Acad. Sci. U. S. A., 112, 12764, 10.1073/pnas.1423041112
Horner-Devine, 2006, Phylogenetic clustering and overdispersion in bacterial communities, Ecology, 87, S100, 10.1890/0012-9658(2006)87[100:PCAOIB]2.0.CO;2
James, 2006, Reconstructing the early evolution of Fungi using a six-gene phylogeny, Nature, 443, 818, 10.1038/nature05110
Jones, 2011, Are there more marine fungi to be described?, Bot. Mar., 54, 343, 10.1515/bot.2011.043
Kurtzman, 2011, 3
Lara, 2010, The environmental clade LKM11 and Rozella form the deepest branching clade of fungi, Protist, 161, 116, 10.1016/j.protis.2009.06.005
Lozupone, 2005, UniFrac: a new phylogenetic method for comparing microbial communities, AEM, 71, 8228, 10.1128/AEM.71.12.8228-8235.2005
Ludwig, 2001
Ludwig, 2004, ARB: a software environment for sequence data, Nucleic Acids Res., 32, 1363, 10.1093/nar/gkh293
Ludwig, 2011, 16 - the use of rRNA gene sequence data in the classification and identification of prokaryotes
Mahe, 2012, PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution, PLoS ONE, 7
Matsen, 2010, pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinform., 11, 10.1186/1471-2105-11-538
Nilsson, 2016, Top 50 most wanted fungi, Mycokeys, 29, 10.3897/mycokeys.12.7553
Panzer, 2015, Data from: identification of habitat-specific biomes of aquatic fungal communities using a comprehensive nearly full-length 18S rRNA dataset enriched with contextual data
Panzer, 2015, Identification of habitat-specific biomes of aquatic fungal communities using a comprehensive nearly full-length 18S rRNA dataset enriched with contextual data, PLoS One, 10, 10.1371/journal.pone.0134377
Peplies, 2008, A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes, Syst. Appl. Microbiol., 31, 251, 10.1016/j.syapm.2008.08.003
Porter, 2008, Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life, Mol. Phylogenet. Evol., 46, 635, 10.1016/j.ympev.2007.10.002
Powell, 2009, Phylogenetic trait conservatism and the evolution of functional trade-offs in arbuscular mycorrhizal fungi, P R Soc. B, 276, 4237, 10.1098/rspb.2009.1015
Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res., 41, D590, 10.1093/nar/gks1219
Rayner, 1987, Regulation of mycelial organization and responses
Reblova, 2016, Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales), IMA Fungus, 7, 131, 10.5598/imafungus.2016.07.01.08
Reich, 2017, How to boost marine fungal research: a first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry, Mar. Genomics, 10.1016/j.margen.2017.09.007
Reich, 2017, Impacts of a reduction in seawater pH mimicking ocean acidification on the structure and diversity of mycoplankton communities, Aquat. Microb. Ecol., 10.3354/ame01831
Rosling, 2011, Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi, Science, 333, 876, 10.1126/science.1206958
Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi, Proc. Natl. Acad. Sci. U. S. A., 109, 6241, 10.1073/pnas.1117018109
Slepecky, 2009, Phenotypic plasticity in fungi: a review with observations on Aureobasidium pullulans, Mycologia, 101, 823, 10.3852/08-197
Stajich, 2009, The fungi, Curr. Biol., 19, R840, 10.1016/j.cub.2009.07.004
Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033
Teeling, 2005, A molecular phylogeny for bats illuminates biogeography and the fossil record, Science, 307, 580, 10.1126/science.1105113
Wang, 2009, A fungal phylogeny based on 82 complete genomes using the composition vector method, BMC Evol. Biol., 9, 10.1186/1471-2148-9-195
Webb, 2008, Phylocom: software for the analysis of phylogenetic community structure and trait evolution, Bioinformatics, 24, 2098, 10.1093/bioinformatics/btn358
Wijayawardene, 2014, Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names, Fungal Divers., 69, 1, 10.1007/s13225-014-0309-2
Wu, 2000, Phylogenetic and biogeographic relationships of eastern Asian and eastern north American disjunct Suillus species (Fungi) as inferred from nuclear ribosomal RNA ITS sequences, Mol. Phylogenet. Evol., 17, 37, 10.1006/mpev.2000.0812
Yarza, 2014, Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences, Nat. Rev. Microbiol., 12, 635, 10.1038/nrmicro3330
Yilmaz, 2014, The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks, Nucleic Acids Res., 42, D643, 10.1093/nar/gkt1209
Yilmaz, 2015, Expanding the world of marine bacterial and archaeal clades, Front. Microbiol., 6, 1524