Dating the molecular clock in fungi - how close are we?

Integration of fungal evolution with the dates of plate tectonic movements, paleoecology, and the evolution of plants and animals requires a molecular clock. Imperfect though they may be, molecular clocks provide the means to convert molecular change into geological time. The relationships among clocks, phylogeography, fossils, and substitution rate variation, along with incorporation of uncertainty into clock estimates are the topics for this commentary. This commentary is timely because, for deeper divergences on the order of hundreds of millions of years, estimates of age of origin are benefiting from increasingly accurate organismal phylogenies and increasingly realistic models of molecular evolution. Taking advantage of Bayesian approaches permitting complex assumptions about node ages and molecular evolution, we used the program BEAST to apply a relaxed lognormal clock analysis to a data set comprising 50 loci for 26 taxa. In the resulting tree, branches associated with nodes calibrated by fossils showed more dramatic substitution rate variation than branches at nodes lacking calibration. As a logical extension of this result, we suspect that undetected rate variation in the uncalibrated parts of the tree is as dramatic as in the calibrated sections, underscoring the importance of fossil calibration. Fortunately, new and interesting fungal fossils are being discovered and we review some of the new discoveries that confirm the ancient origin of important taxa. To help evaluate which fossils might be useful for constraining the ages of nodes, we selected fossils thought to be early members of their clades and used ribosomal or protein-coding gene sequence substitution rates to calculate whether fossil age and expected lineage age coincide. Where ages of a fossil and the expected age of a lineage do coincide, the fossils will be particularly useful in constraining node ages in molecular clock analyses.