DOI: 10.5061/dryad.m7n455k0
title: Data from: Best practices for justifying fossil calibrations

description: 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.
description: Parham et al_Online
 Appendix 1Example of a justified
 calibration from hominin primates: (human-chimpanzee
 node).Parham et al_Online
 Appendix 2Data for Online Appendix
 1 and figure 3.Parham et al_Online
 Appendix 3Examples of justified
 and unjustified fossil calibrations from ‘non-traditional’
 nodes.