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Data from: Best practices for justifying fossil calibrations

Citation

Parham, James F. et al. (2011), Data from: Best practices for justifying fossil calibrations, Dryad, Dataset, https://doi.org/10.5061/dryad.m7n455k0

Abstract

Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates from textbooks (e.g., Dodson 1955). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology. To capitalize on these opportunities, increasingly sophisticated divergence dating methods have been, and continue to be, developed. In contrast, comparatively little attention has been devoted to critically assessing the paleontological and associated geological data used in divergence dating analyses. The lack of rigorous protocols for assigning calibrations based on fossils raises serious questions about the credibility of divergence dating results (Shaul and Graur 2002; Brochu et al. 2004; Graur and Martin 2004; Hedges and Kumar 2004; Reisz and Muller 2004a,b; Theodor, 2004; van Tuinen and Hadly 2004a,b; van Tuinen et al. 2004; Benton and Donoghue 2007; Donoghue and Benton 2007; Parham and Irmis 2008; Ksepka 2009; Benton et al. 2009; Heads 2011). The assertion that incorrect calibrations will negatively influence divergence-dating studies is not controversial. Attempts to identify incorrect calibrations through the use of a posteriori methods are available (e.g., Near and Sanderson 2004; Near et al. 2005; Rutschman et al. 2007; Marshall 2008; Pyron 2010; Dornburg et al. 2011). These methods avoid the need for molecular systematists to interpret the unfamiliar and often obscure literature of paleontology, stratigraphy, and geochronology. Most a posteriori methods assess the consistency among calibrations on different nodes and reject inconsistent calibrations. However, consistency among fossil calibrations (or lack thereof) may be the consequence of temporal or geographical biases in the rock record. For example, all dates could be equally underestimated because of missing rock units or missing fossils in a particular time interval. In these instances, cross validation could lead to the rejection of calibrations that provide a better approximation of divergence times (Marshall 2008; Benton et al. 2009; Lee et al. 2009). We do not deny that a posteriori methods are a useful means of evaluating calibrations, but there can be no substitute for a priori assessment of the veracity of paleontological data.

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