Molecular data is ideal for exploring deep evolutionary history because of its universality, stochasticity and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), independently of morphological evolution, and within a statistical framework that allows testing of evolutionary hypotheses. In particular, molecular data have an important role to play in examining hypotheses concerning the tempo and mode of evolution of animal body plans. Examples are given where molecular phylogenies have led to a re-examination of some fundamental assumptions in metazoan evolution, such as the immutability of early developmental characters, and the evolvability of bauplan characters. Molecular data is also providing a new and controversial timescale for the evolution of animal phyla, pushing the major divisions of the animal kingdom deep into the Precambrian. There have been many reasons to question the accuracy and precision of molecular date estimates, such as the failure to account for lineage-specific rate variation and unreliable estimation of rates of molecular evolution. While these criticisms have been largely countered by recent studies, one problem has remained a challenge: could temporal variation in the rate of molecular evolution, perhaps associated with “explosive” adaptive radiations, cause overestimation of diversification dates? Empirical evidence for an effect of speciation rate, morphological evolution or ecological diversification on rates of molecular evolution is examined, and the potential for rate-variable methods for molecular dating are discussed.
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