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Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data

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Biology of Microfungi

Part of the book series: Fungal Biology ((FUNGBIO))

Abstract

Mycological research, especially research on fungal evolution and ecology, requires a robust and detailed fungal classification and phylogeny to facilitate efficient and informative communication among mycologists as well as for comparative biology relevant to the larger bioscience community. The field of fungal systematics has undergone numerous revisions recently, from early morphological classifications to an integrative taxonomy that is increasingly reliant on molecular phylogeny. These revisions have taken place at a range of taxonomic ranks, fueled by advances surmounting two major challenges, namely, adequate and balanced sampling of genetic markers and taxa and reinterpretation of phylogenetic informativeness of numerous morphological and ecological characters. The Assembling the Fungal Tree of Life (AFTOL) projects reflected a corresponding surge of collaborative effort in fungal molecular phylogeny using PCR and Sanger sequencing. Here we review recent progress in fungal systematics after AFTOL, in the post-Sanger age, and discuss the future fungal systematics that is emerging as a result of the extraordinary volume of data being gathered by high-throughput sequencing. We examine how environmental DNA surveys, sequence-based classification, and phylogenomics and phylotranscriptomics can impact fungal systematics and point out that sequenced fungal genomes could significantly improve multi-marker phylogenetic inference at a range of levels of fungal systematics by facilitating application of phylogenetically informative experimental design. We argue that it is time to integrate fungal systematics, genome-enabled mycology, and other dimensions of fungal research within the framework of evolutionary biology.

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Authors and Affiliations

  1. Department of Biostatistics, Yale School of Public Health, Yale University, 135 College Street, New Haven, CT, 06510, USA

    Zheng Wang Ph.D. & Jeffrey P. Townsend Ph.D.

  2. Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, Göteborg, 405 30, Sweden

    R. Henrik Nilsson Ph.D.

  3. Department of Ecology and Evolutionary Biology, University of Michigan, 1147 Kraus Natural Science Building, 830 North University, Ann Arbor, MI, 48109-1048, USA

    Timothy Y. James Ph.D.

  4. Institute of Microbiology, Beijing Forestry University, Beijing, 100083, China

    Yucheng Dai Ph.D.

  5. Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA

    Jeffrey P. Townsend Ph.D.

  6. Program in Computational Biology and Bioinformatics, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA

    Jeffrey P. Townsend Ph.D.

Authors
  1. Zheng Wang Ph.D.
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  2. R. Henrik Nilsson Ph.D.
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  3. Timothy Y. James Ph.D.
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  4. Yucheng Dai Ph.D.
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  5. Jeffrey P. Townsend Ph.D.
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Corresponding authors

Correspondence to Zheng Wang Ph.D. or Jeffrey P. Townsend Ph.D. .

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Editors and Affiliations

  1. The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT, USA

    De-Wei Li

  2. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China

    De-Wei Li

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Wang, Z., Nilsson, R.H., James, T.Y., Dai, Y., Townsend, J.P. (2016). Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. In: Li, DW. (eds) Biology of Microfungi. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-29137-6_3

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