Calibrated chronograms, fossils, outgroup relationships, and root priors: re-examining the historical biogeography of Geraniales
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We re-examined the recent study by Palazzesi etal., (2012) published in the Biological Journal of the Linnean Society (107: 67-85), that presented the historical diversification of Geraniales using BEAST analysis of the plastid spacer trnL-F and of the non-coding nuclear ribosomal internal transcribed spacers (ITS). Their study presented a set of new fossils within the order, generated a chronogram for Geraniales and other rosid orders using fossil-based priors on five nodes, demonstrated an Eocene radiation of Geraniales (and other rosid orders), and argued for more recent (Pliocene-Pleistocene) and climate-linked diversification of genera in the five recognized families relative to previous studies. As a result of very young ages for the crown of Geraniales and other rosid orders, unusual relationships of Geraniales to other rosids, and apparent nucleotide substitution saturation of the two gene regions, we conducted a broad series of BEAST analyses that incorporated additional rosid fossil priors, used more accepted rosid ordinal topologies, or altered the placement of one fossil Geraniales prior. Our results indicate that their ages are 20-50% too young owing to a combination of (1) strong nucleotide saturation of the DNA regions starting at 65Mya, (2) lack of a root (rosid stem) or other rosid ordinal stem fossil-based priors, (3) the inability of the two DNA regions (with alignment issues) to obtain a monophyletic Geraniales as well as reasonable relationships of Geraniales to other rosid orders, and (4) apparent issues with the nodal placement of a Pelargonium fossil. The Geraniales crown is much older (Campanian of the Cretaceous; 86Mya), the posterior age distribution on all but two fossil nodes are well older than the priors, the placement of a Pelargonium-like fossil is more likely at the crown rather than the stem, but their models of diversification within several clades linked to climatic and orogeny appear supported. We discuss a number of the inherent issues of relaxed-clock dating and outline some 'best practice' approaches for such studies. 2014 The Linnean Society of London.
