Data from: Best practices for justifying fossil calibrations

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.我们将生物演化与气候变化、地质演化及其他历史模式相关联的能力，是理解塑造生物多样性的各类过程的核心前提。将化石记录数据与分子系统发育学（molecular phylogenetics）相结合，是应对这一研究挑战的极具前景的综合研究路径。首个分子分化定年分析（Zuckerkandl与Pauling，1962）以血红蛋白分子的氨基酸差异度量为基础，其替换速率的确定（校准）采用了教科书中不够精准的古生物年代估算值（例如Dodson 1955）。自彼时起，分子序列数据的体量呈爆发式增长，为将分子分化定年方法应用于进化生物学的核心问题提供了愈发广阔的空间。为充分利用这些机遇，愈发精密的分化定年方法已被开发且仍在持续迭代。与之形成对比的是，针对分化定年分析中所使用的古生物及相关地质数据开展批判性评估的研究却相对匮乏。缺乏基于化石的校准严谨规范，这使得分化定年结果的可信度备受质疑（Shaul与Graur 2002；Brochu等2004；Graur与Martin 2004；Hedges与Kumar 2004；Reisz与Muller 2004a、b；Theodor 2004；van Tuinen与Hadly 2004a、b；van Tuinen等2004；Benton与Donoghue 2007；Donoghue与Benton 2007；Parham与Irmis 2008；Ksepka 2009；Benton等2009；Heads 2011）。‘错误的校准会对分化定年研究产生负面影响’这一论断并无争议。目前已有通过后验（a posteriori）方法识别错误校准的相关尝试（例如Near与Sanderson 2004；Near等2005；Rutschman等2007；Marshall 2008；Pyron 2010；Dornburg等2011）。这些方法无需分子系统学家去解读陌生且往往晦涩的古生物学、地层学（stratigraphy）与地质年代学（geochronology）文献。多数后验方法会评估不同系统发育节点上的校准之间的一致性，并剔除不一致的校准项。然而，化石校准间的一致性（或不一致性）或许源于岩石记录中的时间或地理偏差。例如，由于特定时间区间内缺失岩层或化石，所有定年结果可能均被同等低估。在此类情形下，交叉验证（cross validation）可能会剔除那些能更准确反映分化时间的校准项（Marshall 2008；Benton等2009；Lee等2009）。我们并不否认后验方法是评估校准的有效手段，但古生物数据真实性的先验（a priori）评估，始终是无可替代的。