Dating clades with fossils and molecules: the case of Annonaceae

This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the principles and problems of placing fossils in trees of extant taxa and using them to constrain the ages of nodes in molecular dating analyses. Endressinia and Futabanthus provide minimum ages of 112 Mya for the stem lineage and 89 Mya for the crown group of Annonaceae, and the diversity of endosperm ruminations in seeds from the London Clay indicates that the four main clades of Annonaceae had diverged by 50 Mya. Ages inferred using these minimum constraints and a plastid phylogenetic tree for Annonaceae, particularly crown ages of the two main clades (Malmeoideae and Annonoideae), depend on assumptions regarding the pattern of variation in rates of molecular evolution. Our results using methods that assume rate autocorrelation or log‐normal distribution of rates suggest that neither assumption fits well the apparently abrupt changes in rates in Annonaceae. Instead of soft‐bounded age constraints, we argue for the use of only well‐substantiated fossil evidence by means of priors with hard bounds. Thus, we can infer ages that take into account both palaeontological and phylogenetic uncertainty, without confounding the different factors involved. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society , 2012, 169 , 84–116.