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Fungi Evolution Revisited: Application of the Penalized Likelihood Method to a Bayesian Fungal Phylogeny Provides a New Perspective on Phylogenetic Relationships and Divergence Dates of Ascomycota Groups

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Abstract

The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous Ascomycetes and probably maintain ancestor characters since their representatives are intermingled among other filamentous fungi. Also, we show that the evolutionary rate heterogeneity within Ascomycota precludes the assumption of a global molecular clock. Accordingly, we used the penalized likelihood method, and for calibration we included a 400 million-year-old Pyrenomycete fossil considering two distinct scenarios found in the literature, one with an estimated date of 1576 Myr for the plant–animal–fungus split and the other with an estimated date of 965 Myr for the animal–fungus split. Our data show that the current classification of the fossil as a Pyrenomycete is not compatible with the second scenario. Estimates under the first scenario are older than dates proposed in previous studies based on small subunit rDNA sequences but support estimates based on multiprotein analysis, suggesting that the radiation of the major Ascomycota groups occurred into the Proterozoic era.

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Acknowledgments

We thank Beatriz Schnabel for excellent technical assistance and help with the artwork. A.C.B.P. received a fellowship from FAPESP (Brazil). G.F.O.S. was supported by a Howard Hughes Medical Institute Post-Doctoral Fellowship (USA). A.B. received grants from FAPESP (Brazil) and M.R.S.B. received grants from FAPESP and CNPq (Brazil) and the International Research Scholars Program of the Howard Hughes Medical Institute (USA).

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  1. Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil

    Ana Carolina B. Padovan, Gerdine F.O. Sanson, Adriana Brunstein & Marcelo R.S. Briones

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  1. Ana Carolina B. Padovan
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  2. Gerdine F.O. Sanson
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  3. Adriana Brunstein
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  4. Marcelo R.S. Briones
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Correspondence to Adriana Brunstein.

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Reviewing Editor: Dr. Nicolas Galtier

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Padovan, A.C.B., Sanson, G.F., Brunstein, A. et al. Fungi Evolution Revisited: Application of the Penalized Likelihood Method to a Bayesian Fungal Phylogeny Provides a New Perspective on Phylogenetic Relationships and Divergence Dates of Ascomycota Groups. J Mol Evol 60, 726–735 (2005). https://doi.org/10.1007/s00239-004-0164-y

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