Purple haze: Cryptic purple sequestrate <i>Cortinarius</i> in New Zealand

Nilsen, Andy R.; Wang, Cecilia; Soop, Karl; Cooper, Jerry A.; Ridley, G. S.; Wallace, Michael; Summerfield, Tina C.; Brown, Chris M.; Orlovich, David A.

doi:10.1080/00275514.2020.1730120

Cited by 11 publications

(5 citation statements)

References 42 publications

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“…2018), and species hypotheses represented by single sequences were included. We modified a small number of entries in the UNITE database to reflect recent taxonomic updates of particular Cortinarius species by Nilsen et al . (2020) and Nilsen et al .…”

Section: Methodsmentioning

confidence: 99%

Different factors drive community assembly of rare and common ectomycorrhizal fungi

Galen¹,

Orlovich²,

Lord³

et al. 2022

Preprint

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Understanding what drives community assembly processes and how communities respond to environmental gradients are fundamental goals in community ecology. Ectomycorrhizal fungi support major forest systems across the globe, but the diversity, distribution and environmental controls affecting ectomycorrhizal community composition are unknown in many regions, particularly in the southern hemisphere. Here we investigate the assembly of ectomycorrhizal fungal communities based on eDNA samples from 81 Nothofagus forests across New Zealand's South Island. We apply zeta diversity analysis and multi-site generalised dissimilarity modelling (MS-GDM) to investigate assembly patterns and quantify the effects of 43 biotic and environmental variables on community turnover. The zeta diversity MS-GDM framework differentiates between the environmental factors driving turnover of rare and common species, so provides a more complete picture of community dynamics than traditional beta diversity analyses. Results showed that community assembly was dominated by deterministic rather than stochastic processes. Soil variables were important drivers across the full range of rare, intermediate and common species. Ground cover variables, forest patch size and rainfall had greater effects on turnover of rare species, whereas temperature variables and host tree size had greater effects on common species turnover. Applying these methods for the first time to fungi demonstrates that there are distinct differences in the ecological processes affecting different aspects of the ectomycorrhizal community, which has important implications for understanding the functional effects of community responses to environmental change.

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Section: Methodsmentioning

confidence: 99%

Different factors drive community assembly of rare and common ectomycorrhizal fungi

Galen¹,

Orlovich²,

Lord³

et al. 2022

Preprint

Self Cite

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“…ASVs were putatively named using the "assign-Taxonomy" function with the UNITE database version 8.3 general release FASTA file (Kõljalg et al, 2020;Nilsson et al, 2018) as the reference database (including species hypotheses represented by single sequences), with the default minimum bootstrap confidence level of 50 for assigning a taxonomic level. We modified a small number of entries in the UNITE database to reflect recent taxonomic updates by Nilsen et al (2020) and Nilsen et al (2021) (Table S1). In total, 54% of ASVs were assigned taxonomy to family level, 43.6% to genus level and 19.6% to species level.…”

Section: Fungal Identificationmentioning

confidence: 99%

Zeta diversity differentiates factors driving community assembly of rare and common ectomycorrhizal fungi

et al. 2023

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A fundamental goal in community ecology is to understand what factors drive community assembly processes. The factors affecting ectomycorrhizal fungal communities are unknown in many regions, particularly in the southern hemisphere. We investigate community assembly using ITS2 metabarcoding of ectomycorrhizal fungi sampled from 3943 hyphal ingrowth bags buried in 81 Nothofagus forests across New Zealand's South Island. By applying zeta diversity analysis and multisite generalized dissimilarity modelling (MS‐GDM) we quantify the effects of 43 biotic and environmental variables on community turnover. Unlike traditional beta diversity analyses that are heavily influenced by rare species, the zeta diversity framework differentiates between factors driving turnover of rare and common species, providing a more complete picture of community dynamics. We found that community assembly was dominated by deterministic rather than stochastic processes and identified ecological factors affecting all taxa, as well as others that were specifically important to rare or common taxa. Soil variables were important drivers of turnover for all species, whereas ground cover variables, forest patch size, precipitation and host tree identity had greater effects on rarer species, and tree size and temperature effects were specific to more common species. Interestingly, the effect of temperature on common species is in line with recent evidence from other Kingdoms, pointing to possible generality, and highlighting the importance of considering common species. Applying these methods to fungi has allowed us to identify the distinct ecological processes that structure rare and common taxa during community assembly. This has important implications for understanding the functional effects of community responses to environmental change.

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“…Species identification in Agaricales has traditionally relied on morphological characters (e.g., Singer 1986;Bas et al 1988;Horak 2005;Knudsen and Vesterholt 2008) that are known to be subject to parallel evolution and phenotypic plasticity (Slepecky and Starmer 2009). In many cases, separation of species based on morphology alone is challenging and many taxa represent complexes with (pseudo)cryptic species (Geml et al 2006;Bickford et al 2007;Carriconde et al 2008;Stefani et al 2014;Balasundaram et al 2015;Guo et al 2016;Sánchez-García et al 2016;Li et al 2017;Peintner et al 2019;Vizzini et al 2019a, b;Nilsen et al 2020;Sato et al 2020;Voitk et al 2020). Putative interspecific hybridization events have been suggested to occur in some Agaricales (Aanen et al 2000;Hughes et al 2013).…”

Section: Species Concepts and Species Recognitionmentioning

confidence: 99%

“…Regarding sequence-based molecular methods, ITS is still the most widely used marker for species identification within Agaricales (Badotti et al 2017;Yang et al 2018;Vu et al 2019;Kalichman et al 2020). It is quite easy to amplify and sequence, even from old specimens-up to 200 years old (Larsson and Jacobsson, 2004;Liimatainen et al 2014Liimatainen et al , 2020Nilsen et al 2020). ITS has been found to be a suitable barcode for some groups in the Agaricales, including the genera Amanita (e.g., Vizzini et al 2016b;Cui et al 2018;Saba et al 2019;Hanss and Moreau 2020), Cortinarius (e.g., Frøslev et al 2005Frøslev et al , 2007Frøslev et al , 2017Liimatainen et al 2014Liimatainen et al , 2020Stefani et al 2014;Garnica et al 2016;Nilsen et al 2020), Entoloma (Dima et al 2021), Gymnopilus (Thorn et al 2020), Hebeloma (Eberhardt et al 2013, Lepista (Wang et al 2019), Marasmius (Shay et al 2017;Haelewaters et al 2020a), Melanoleuca (Vizzini et al 2011;Antonín et al 2014Antonín et al , 2015Antonín et al , 2017, Tricholoma (Jargeat et al 2010;Heilmann-Clausen et al 2017), Tricholomopsis (Holec and Kolařík 2012;Cooper and Park 2016), and the families Agaricaceae (Justo et al 2015;Vizzini et al 2014aVizzini et al , b, 2019a, Lyophyllaceae…”

Section: Species Concepts and Species Recognitionmentioning

confidence: 99%

Delimiting species in Basidiomycota: a review

et al. 2021

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Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.

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Purple haze: Cryptic purple sequestrate Cortinarius in New Zealand

Cited by 11 publications

References 42 publications

Different factors drive community assembly of rare and common ectomycorrhizal fungi

Different factors drive community assembly of rare and common ectomycorrhizal fungi

Zeta diversity differentiates factors driving community assembly of rare and common ectomycorrhizal fungi

Delimiting species in Basidiomycota: a review

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