High-Level Classification of the Fungi and a Tool for Evolutionary Ecological Analyses
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Fungal Diversity (2018) 90:135–159 https://doi.org/10.1007/s13225-018-0401-0 (0123456789().,-volV)(0123456789().,-volV) High-level classification of the Fungi and a tool for evolutionary ecological analyses 1,2,3 4 1,2 3,5 Leho Tedersoo • Santiago Sa´nchez-Ramı´rez • Urmas Ko˜ ljalg • Mohammad Bahram • 6 6,7 8 5 1 Markus Do¨ ring • Dmitry Schigel • Tom May • Martin Ryberg • Kessy Abarenkov Received: 22 February 2018 / Accepted: 1 May 2018 / Published online: 16 May 2018 Ó The Author(s) 2018 Abstract High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomoph- thoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set. Keywords 51 new taxa Á Species Hypothesis Á Taxonomy of fungi Á Phylogenetic classification Á Subkingdom Á Phylum Á Nucleariae Á Ascomycota Á Aphelidiomycota Á Basidiobolomycota Á Basidiomycota Á Blastocladiomycota Á Calcarisporiellomycota Á Chytridiomycota Á Entomophthoromycota Á Entorrhizomycota Á Glomeromycota Á Kickxellomycota Á Monoblepharomycota Á Mortierellomycota Á Mucoromycota Á Neocallimastigomycota Á Olpidiomycota Á Rozellomycota Á Zoopagomycota Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13225-018-0401-0) contains supplementary material, which is available to authorized users. 6 Global Biodiversity Information Facility, Copenhagen, & Leho Tedersoo Denmark [email protected] 7 Department of Biosciences, University of Helsinki, Helsinki, 1 Natural History Museum, University of Tartu, 14a Ravila, Finland 50411 Tartu, Estonia 8 Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, 2 Institute of Ecology and Earth Sciences, University of Tartu, VIC 3004, Australia 14a Ravila, 50411 Tartu, Estonia 3 Estonian Young Academy of Sciences, 6 Kohtu, Tallinn, Estonia 4 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada 5 Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyva¨gen 18D, 75236 Uppsala, Sweden 123 136 Fungal Diversity (2018) 90:135–159 Introduction 2014; Maestre et al. 2015). For better comparability across fungi and preferably across all organisms, taxonomic ranks Fungi are one of the largest groups of eukaryotes that play should be monophyletic and exhibit at least roughly similar key roles in nutrient and carbon cycling in terrestrial age (Hennig 1966; Avise and John 1999; Yilmaz et al. ecosystems as mutualists, pathogens and free-living 2014; Samarakoon et al. 2016; Hyde et al. 2017; Tedersoo saprotrophs (McLaughlin and Spatafora 2014). Because 2017a). For example, orders and classes in chytrids and many fungi are unculturable and seldom produce visible zygomycetes should ideally correspond to these ranks in sexual structures, molecular techniques have become Dikarya. So far, the class rank is little used and orders are widely used for taxonomic detection of species to under- non-corresponding in most early-diverging lineages such as stand shifts in their richness and composition along envi- Chytridiomyceta, Rozellomyceta, Zoopagomyceta, etc. ronmental gradients (Persˇoh 2015; Balint et al. 2016; This is due to great differences in the described richness, an Tedersoo and Nilsson 2016). Accurate taxonomic identifi- order of magnitude different number of taxonomists cation to species, genera and higher taxonomic levels is a working on these groups and the abundance of phyloge- key for reliable assignment of ecological and functional netically informative morphological and ecophysiological traits to taxa for further ecophysiological and biodiversity characters (Samarakoon et al. 2016). A number of re- analyses (Ko˜ljalg et al. 2013; Jeewon and Hyde 2016; classifications have been performed in Pucciniomycotina Nguyen et al. 2016; Edgar 2017; Tedersoo and Smith and Agaricomycotina to make the constituent orders and 2017). Furthermore, molecular methods have revolution- classes correspond to those in Ascomycota (Doweld 2001; ized our understanding concerning phylogenetic relation- Bauer et al. 2006). Using divergence time in ranking taxa ships among the Fungi and have substantially altered the has recently gained popularity in mycology, but these morphology-based classification system (Hibbett et al. studies focus on specific phyla, classes or lower-level taxa 2007; Wijayawardene et al. 2018). Availability of full- (Hongsanan et al. 2017; Liu et al. 2016; Zhao et al. length rRNA gene and protein-encoding marker gene 2016, 2017; Hyde et al. 2017). sequences (James et al. 2006a) and evolution of high-res- Although plant and fungal taxonomists follow the cri- olution genomics tools (Spatafora et al. 2016, 2017) has terion of monophyly (i.e. taxa share an exclusive common further refined the order of divergence and classification of ancestor), this is commonly violated in higher-level clas- the major fungal groups (e.g. Zhao et al. 2017). sification of eukaryotes (including fungal phyla) as many Species-level molecular identification of fungi takes of the high-ranking taxa are intentionally maintained poly- advantage of the Internal Transcribed Spacer (ITS) region or paraphyletic (such as Choanozoa in Fig. 1; e.g. Cavalier- of ribosomal RNA (rRNA) gene (Gardes and Bruns 1996; Smith 2013; Ruggiero et al. 2015). Because of different Ko˜ljalg et al. 2005; Schoch et al. 2012; Nilsson et al. 2014). resolution and poor correspondence of ranks among phyla The ITS region is not, however, reliably alignable across in terms of evolutionary time, the modern fungal classifi- families and higher taxa, which renders large-scale phy- cation systems of Species Fungorum (www.spe logenetic approaches and testing evolutionary ecological ciesfungorum.org), MycoBank (www.mycobank.org), hypotheses (cf. Cavender-Bares et al. 2009) impossible. UNITE (Abarenkov et al. 2010), Faces of Fungi (Jayasiri Information concerning phylogenetic distance among fun- et al. 2015), International Nucleotide Sequence Databases gal taxa in communities enables to detect relatively subtle consortium (https://www.ncbi.nlm.nih.gov/taxonomy), Adl shifts in diversity and better understand community et al. (2012), Cavalier-Smith et al. (2014) and Ruggiero assembly processes (Fouquier et al. 2016). Using rRNA et al. (2015) do not fully satisfy the expectations of ecol- 18S gene sequences, Maherali and Klironomos (2007) ogists and biodiversity researchers. demonstrated that phylogenetically overdispersed commu- The objective of this initiative is to develop the fungal nities promote biomass strongest, but growth benefits of classification as a user-friendly tool for both taxonomists arbuscular mycorrhizal fungi are phylogenetically con- and ecologists. We propose an updated higher-level clas- served. Rousk et al. (2010) showed that soil pH has a sification scheme for the Fungi and a backbone classifica- strong effect on fungal and bacterial phylogenetic compo- tion tree that accounts for published phylogenies, sition on a local scale. divergence times and monophyly criterion. We also present Depending on the target group of organisms and taxo- a bioinformatics routine that can be utilized in evolutionary nomic resolution, plant, microbial and fungal ecologists ecological studies using any classification scheme and typically test the importance of environmental variables on organism group. To demonstrate its usefulness in fungal diversity at the level of orders, classes or phyla, but addressing complementary research questions, we provide not their subranks or various ranks intermixed due to an example about testing evolutionary hypotheses in a simplicity and avoiding confusion (e.g. Tedersoo et al. global ITS-based high-throughput sequencing data set. 123 Fungal Diversity (2018) 90:135–159 137 Sub- the average [ 3-fold were removed from the alignment, Kgd. kgd. Phyl. Cl. Metazoa=Animalia because these destabilized the phylogeny via long branch a Choanoflagellida attraction (available as Online Resource 1). The final data Filasteriae Holozo Ichthyosporidia nozoa set was comprised of 90 terminals and 5296 characters, 1 Nuclearida Kingdom which was subjected to ML analysis with 1000 bootstrap 1 Fonticulida }Nucleariae } Choa replicates and molecular clock analysis using BEAST v2.4. Basal clone group 2 Clade GS01 (Bouckaert et al. 2014). To compare the phylogenetic Basal clone group 1 congruence among phyla, we also used alignments of nd Rozellomycota Rozello- myceta James et al. (2006a) for RNA Polymerase II subunits 1 Microsporidea (Cl) } phisto- poridia Aphelidio- (RPB1) and 2 (RPB2) and Translation Elongation Factor