title: Molecular dating, evolutionary rates, and the age of the grasses.
abstract: Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae ∼51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI 02912, USA; Department of Biology & Burke Museum of Natural History and Culture, University of Washington, 24 Kincaid Hall, Seattle, WA 98195, USA; Department of Ecology and Evolution, Biophore, Quartier Sorge, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Pascal-Antoine
authors.initials: PA
authors.lastname: Christin
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Spriggs
authors.forename: Colin P
authors.initials: CP
authors.lastname: Osborne
authors.forename: Caroline A E
authors.initials: CA
authors.lastname: Strömberg
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
authors.forename: Erika J
authors.initials: EJ
authors.lastname: Edwards
mesh_terms: D018745:Genome, Plant / Q000235:genetics; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D006109:Poaceae / Q000145:classification* / Q000235:genetics*; D013995:Time
keywords: Poaceae; divergence time; molecular dating; mutation rate; phylogeny