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How model assumptions affect our understanding of the evolution of ectomycorrhizal symbiosis in fungi


Sheikh, Sanea; Khan, Faheema; Bahram, Mohammad; Ryberg, Martin (2021), How model assumptions affect our understanding of the evolution of ectomycorrhizal symbiosis in fungi, Dryad, Dataset,


The kingdom of Fungi comprises one of the most diverse set of functions and species. Fungi are heterotrophic and can obtain their nutrients from living organisms (biotrophic) or dead matter (saprotrophic). One of the most common biotrophic lifestyles is mycorrhizal association, including ectomycorrhiza (ECM) that involves the largest number of mycorrhizal fungi and is essential for nutrient uptake and health of many stand forming trees. Despite our growing understanding of the diversity of ECM fungi, the evolutionary history of ECM is still unresolved. There are two conflicting views about the evolution of ECM in fungi suggesting (1) relatively few transitions to ECM followed by reversals to saprotrophy, or (2) at least 78 independent origins and no reversals of ECM. In this study, we investigate the evolution of ECM and test if reversals to a saprotrophic lifestyle are likely. We assembled a dataset of 2,174 fungal taxa covering the three subphyla that include ECM fungi: Agaricomycotina, Mucoromycotina and Pezizomycotina. We created a time-calibrated phylogeny using TreePL for a concatenated dataset of five marker gene sequences (nuc58, nucLSU, nucSSU, rpb1, and rpb2). The fit of different evolutionary processes to the pattern of ECM fungal taxa in the tree was compared using model-based methods, including models with variable rates in clades or through time. We find that models implementing variable rates through clades or time are a better fit than models without rate shifts. We further find that the conclusion about the relative rate between ECM and non-ECM depends largely on whether rate shifts are allowed or not. We conclude that standard constant rate ancestral state reconstruction models are not adequate for the analysis of the evolution of ECM fungi, and may give contradictory results to more extensive analyses.