Phylogenetic Diversity and Evolutionary History of Fungi

Fungi represent one of the most ancient and diverse branches of the eukaryotic tree of life, with origins tracing back over a billion years. Through the integration of molecular phylogenetics, fossil calibration and comparative genomics, a coherent picture has emerged in which major fungal lineages diversified in concert with terrestrial plants and shifting climates. Early divergences gave rise to flagellated chytrids and zygomycete‐like groups, followed by the crown radiation of the Dikarya—Ascomycota and Basidiomycota—during the Paleozoic and Mesozoic eras. Time‐calibrated trees reveal repeated bursts of speciation linked to key innovations such as the pileate-stipitate fruiting body, saprotrophic degradation of complex substrates and the independent evolution of symbiotic lifestyles. The establishment of ectomycorrhizal and endophytic associations provided ecological opportunities that fuelled explosive diversification in several classes. Fossil discoveries extending back to the Devonian document early plant-pathogenic and saprotrophic interactions, offering minimum age constraints for major nodes. Together, these lines of evidence illuminate the global significance of fungi as decomposers, mutualists and pathogens, and underpin practical applications in forestry, agriculture and biotechnology.

Research from Nature Portfolio

Recent studies have described a well-preserved asexual fungus from the Rhynie Chert (circa 407 Ma) that forms conidiophores on an early lycopsid host and induces distinctive plant tissue reactions. This extinct ascomycete lineage provides a robust calibration point for the origin of Dikarya and offers direct insight into early plant-fungus pathogenic interactions. In a complementary megaphylogenetic analysis incorporating over 5 200 species of Agaricomycetes, researchers have reconstructed a dated, class-wide tree revealing a rapid Jurassic radiation coincident with the spread of (sub)tropical coniferous forests. Morphological innovation of the pileate-stipitate fruiting body emerged repeatedly as a key driver of lineage diversification, while subsequent Cretaceous and Paleogene clade-specific radiations reflect both mass extinction events and the rise of angiosperm-dominated ecosystems.

Phylogenetic Diversity and Evolutionary History of Fungi publication trend

The graph below shows the total number of articles in phylogenetic diversity and evolutionary history of fungi across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenetic diversity: A measure of evolutionary breadth in a group, calculated from the sum of branch lengths in a phylogenetic tree.

Dikarya: The fungal subkingdom comprising Ascomycota and Basidiomycota, united by a prolonged dikaryotic stage in the life cycle.

Ectomycorrhizal symbiosis: A mutualistic association in which fungal hyphae form a sheath around plant roots, enhancing nutrient uptake and soil stability.

Molecular clock analysis: A method for estimating the timing of evolutionary divergences based on calibrated rates of genetic mutation.

Pileate-stipitate morphology: A fruiting body form characterised by a distinct cap (pileus) mounted on a stalk (stipe), typical of many mushroom-forming fungi.

References

1. A fungal plant pathogen discovered in the Devonian Rhynie Chert. Nature Communications (2023).
2. Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology & Evolution (2019).
3. The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes. New Phytologist (2023).
4. Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae). Frontiers in Microbiology (2022).
5. The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation. IMA Fungus (2020).
6. Contemporaneous radiations of fungi and plants linked to symbiosis. Nature Communications (2018).