A timetree of Fungi dated with fossils and horizontal gene transfers

Lénárd, L. Szánthó and Merényi, Zsolt and Philip, Donoghue and Toni, Gabaldón and Nagy, László and Szöllősi, Gergely and Eduard, Ocaña-Pallarès (2025) A timetree of Fungi dated with fossils and horizontal gene transfers. NATURE ECOLOGY & EVOLUTION, 9. pp. 1989-2001. ISSN 2397-334X

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Abstract

Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phylogenetic markers and accounting for across-site compositional heterogeneity in amino acid sequences. To address uncertainties in fungal dating, we sampled chronograms from four relaxed molecular clock analyses, each integrating distinct sets of calibrations and relative time-order constraints. The first analysis used a core set of 27 calibrations alongside 17 relative constraints derived from fungi-to-fungi horizontal gene transfer events. Three further analyses extended this core set with additional timing information identified in our reevaluation of the evolution of pectin-specific enzymes in Fungi. Our timetree, integrating analytic uncertainties, suggests older ages for crown Fungi (1,401–896 Ma) than recently reported, providing a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma). This supports a protracted gap between the onset of these interactions and the rise of modern land plants. Altogether, our study provides a refined timescale for fungal diversification and a temporal framework for future investigations into early interactions involving fungi and the algal ancestors of embryophytes.

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