Evolution of Fungi

by

David Hibbett

• LAST REVIEWED: 13 January 2014
• LAST MODIFIED: 13 January 2014
• DOI: 10.1093/obo/9780199941728-0046

Introduction

Fungi make up a major clade of eukaryotes that includes yeasts, molds, lichens, and mushrooms. The ancestor of Fungi was probably a flagellated, aquatic unicellular organism, but the group is now dominated by terrestrial, filamentous forms that lack flagella. Fungi obtain nutrition as saprotrophs (decomposers) or biotrophs (mutualists and parasites). Fungi play a critical role in the carbon cycle and have huge economic impacts as decayers, pathogens, and industrial microorganisms. For much of the history of mycology, the only characters available for estimating evolutionary relationships of Fungi were macromorphology (for groups that produce macroscopic structures, such as mushrooms) and anatomical features (e.g., shapes and staining reactions of spores). Starting in the 1960s, electron microscopy made it possible to observe subcellular characters, such as features associated with flagella or the mitotic apparatus, which were used to address the higher-level relationships and the limits of Fungi. Until the late 20th century, fungal systematists routinely developed phylogenetic hypotheses and classifications through subjective analyses of nonmolecular characters, but they rarely applied cladistic methods. After the Polymerase Chain Reaction (PCR) was developed in the late 1980s, however, mycologists turned toward analyses of DNA characters, particularly ribosomal RNA (rRNA) gene sequences. Many of the older anatomy-based hypotheses were upheld by analyses of molecular data, but there were also surprises, particularly involving morphologically cryptic taxa (e.g., yeasts) or highly derived forms that lack informative anatomical characters (e.g., gasteromycetes, such as stinkhorns and puffballs). Around the beginning of the 21st century, multilocus phylogenetic analyses using PCR amplification of protein-coding as well as rRNA genes became standard, which combined dense taxon sampling with moderately large numbers of molecular characters. Currently, fungal systematics is being further transformed by analyses of whole genomes and environmental DNA sequences (metagenomics). The following sections emphasize recent progress in reconstructing fungal phylogenetic relationships through the use of molecular characters, with reference to selected older works that describe the taxonomic diversity, ecology, and functional biology of Fungi in detail. Applications of fungal phylogenetics in analyses of horizontal gene transfer and molecular clock dating are also reviewed, along with estimates of the number of fungal species and the impact of cryptic species on understanding fungal diversity. Future additions to this bibliography will address the evolution of specific morphological and ecological traits in Fungi.

Introductory Works for Students, Teachers, and the General Public

For general introductions to Fungi, including ethnomycology and practical uses of Fungi, lay readers are directed to the accessible but scientifically rich texts in Hudler 2000 and Petersen 2013. The fungal pages on the Tree of Life Web Project (Blackwell, et al. 2012, cited under Textbooks and Major Taxonomic References) also offer a user-friendly overview of the group, emphasizing evolution. Most college-level general biology textbooks, such as Sadava, et al. 2012, provide an information-rich introduction to fungal biology. In fact, because introductory biology textbooks are revised frequently, they often provide more up-to-date treatments of the broad outlines of fungal phylogeny than current editions of mycology textbooks. Many good mushroom field guides are available, but most have little, if any, content related to evolution, so they are not cited here. However, three websites aimed at amateur mycologists, students, and teachers are listed, because they all have sections that touch on evolution of macrofungi (mushrooms). Tom Volk’s Fungi, MykoWeb, and MushroomExpert.com each illustrate how mycology and evolutionary biology are reaching students and citizen-scientists. A review of the highly accessible resources cited here should prepare (and motivate) those who are interested to delve further into the more technical works cited under Textbooks and Major Taxonomic References.

• Hudler, George W. 2000. Magical mushrooms, mischievous molds. Princeton, NJ: Princeton Univ. Press.

  This compact volume provides an engaging introduction to the diversity of Fungi, their ecological roles, and their often-profound impacts on human affairs. The higher-level taxonomy is out of date, but this does not detract from the intriguing descriptions of fungal biology.

• MushroomExpert.com.

  This website, produced by Michael Kuo, emphasizes taxonomy and identification using macro- and microscopic characters. A well-hidden collection of “Articles and Miscellany” contains an essay titled “The Evolution of a Great-Big Headache” that addresses the impact of molecular phylogenetics on mushroom taxonomy, from the unique perspective of the author.

• MykoWeb.

  This site, produced by Michael Wood and associated with the Mycological Society of San Francisco, includes many beautiful images of the mushrooms of California, as well as a section titled “Systematics” that includes notes on molecular phylogenetics (of macrofungi).

• Petersen, Jens H. 2013. The kingdom of Fungi. Princeton, NJ: Princeton Univ. Press.

  Lavishly illustrated, with spare, economical text, this new book draws readers into the world of Fungi and revels in their astonishing diversity. Stunning macro- and microphotographs are supplemented with simple phylogenetic tree diagrams. An excellent counterpart to the Hudler 2000 text.

• Sadava, David, David M. Hillis, H. Craig Heller, and May Berenbaum. 2012. Life: The science of biology. 10th ed. New York: Freeman.

  A college-level general biology textbook with one chapter that provides an introduction to Fungi (also discussed in other chapters).

• Tom Volk’s Fungi.

  Tremendously rich resource on fungal diversity, including numerous “Fungus of the Month” pages, many with evolutionary themes.