High-level classification of the Fungi and a tool for evolutionary ecological analyses

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, Entomophthoromycota, 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.

Characterization of the mycobiome of the seagrass,Zostera marina, reveals putative associations with marine chytrids

“…The prevalence of unclassifiable ASVs, many of which have closest matches in the Chytridiomycota and Aphelidomycota, with Z. marina makes sense given that these lineages have been previously observed to be the dominant fungal lineages in the marine and aquatic ecosystems (Comeau et al, 2016; Grossart et al, 2019; Picard, 2017; Richards et al, 2012, 2015; Rojas-Jimenez et al, 2019) and have life histories that include associations with green algae (Letcher et al, 2013; Picard et al, 2013; Tedersoo et al, 2018). Thus, it is likely that seagrasses, as marine plants, may be providing these fungal lineages with a new ecological niche.…”

Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria

“…In brief, the following studies were used to extract much of the class to domain level classification information: Yoon et al (2006), Ruhfel et al (2014), Magallon et al (2015), Leliaert et al (2017) (Archaeplastida); Fiore-Donno et al (2010), Lahr et al (2013), Cavalier-Smith et al (2015b, 2016), Tekle et al (2016), Kang et al (2017), Tekle & Wood 2017 (Amoebozoa); Kolisko 2011, Kamikawa et al (2014), Radek et al (2014), Cavalier-Smith (2016), Yubuki et al (2017) (Excavata); Grant et al (2009), Riisberg et al (2009), Brown & Sorhannus (2010), Yang et al (2012), Cavalier-Smith & Scoble (2013), Shiratori et al (2015, 2017), Yubuki et al (2015), Aleoshin et al (2016), Derelle et al (2016), Dumack (2016), Gao et al (2016), Krabberød et al 2017, Reñé et al (2017) (Harosa); Brown et al (2009, 2013), Cavalier-Smith & Chao (2010), Zhang (2011), Glücksman et al (2013), Nosenko et al 2013, Paps et al (2013), Yabuki et al (2013), Telford et al 2015; Torruella et al (2015), Whelan et al (2015), Corsaro et al (2016), Carr et al (2017), Dohrmann & Wöhrheide (2017), Hehenberger et al (2017), Schiffer et al (2017), Simion et al (2017), Tedersoo et al (2018), (Opisthokonta); Yoon et al (2008, 2011), Wegener Parfrey et al (2010, 2011), Burki et al (2012, 2016), Cavalier-Smith & Chao (2012), Yabuki et al (2012, 2014) Cavalier-Smith et al (2014, 2015a), Burki (2014), Katz & Grant (2014), Sharpe et al (2015), Brown et al (2017) (minor groups and all eukaryotes). Following the divergence time estimates of Wegener Parfrey et al (2011), kingdoms and phyla were assigned to higher taxa that diverged roughly at >1000 and 542 Mya (as described for fungi in Tedersoo et al 2018). These criteria were used to make the latest divergi...…”

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

“…(2) Current state of the fungal tree of life Despite various hurdles, not least an unwieldy diversity of largely unknown fungal species, mycologists have been building a classification that reflects evolutionary relationships (Hibbett et al, 2007Schoch et al, 2009;McLaughlin & Spatafora, 2014;Spatafora et al, 2016;Tedersoo et al, 2018). Developing and refining this classification is critical for predicting clade properties including shared history of ecological guilds and functional traits.…”