Article

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.

Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil.
Journal of Molecular Evolution (Impact Factor: 1.86). 07/2005; 60(6):726-35. DOI: 10.1007/s00239-004-0164-y
Source: PubMed

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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    • "It is enclosed in Devonian Rhynie Chert dating back 410 million years (Taylor et al., 2005). P. devonicus was often assigned to Sordariomycetes, but its exact systematic position is disputed (Taylor et al., 2005; Eriksson, 2005; Padovan et al., 2005; Taylor and Berbee, 2006). An assignment to the Pezizomycetes seems also possible, since Paleopyrenomycites might have produced operculate asci (Lücking et al., 2009). "
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    • "It is enclosed in Devonian Rhynie Chert dating back 410 million years (Taylor et al., 2005). P. devonicus was often assigned to Sordariomycetes, but its exact systematic position is disputed (Taylor et al., 2005; Eriksson, 2005; Padovan et al., 2005; Taylor and Berbee, 2006). An assignment to the Pezizomycetes seems also possible, since Paleopyrenomycites might have produced operculate asci (Lücking et al., 2009). "
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    • "It is enclosed in Devonian Rhynie Chert dating back 410 million years (Taylor et al., 2005). P. devonicus was often assigned to Sordariomycetes, but its exact systematic position is disputed (Taylor et al., 2005; Eriksson, 2005; Padovan et al., 2005; Taylor and Berbee, 2006). An assignment to the Pezizomycetes seems also possible, since Paleopyrenomycites might have produced operculate asci (Lücking et al., 2009). "
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    ABSTRACT: The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent four major ascomycete lineages (Lecanoromycetes, Laboulbeniomycetes, Dothideomycetes, and Eurotiomycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing all main groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of ascomycetes in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises such as mass extinctions and rapidly recovered.
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