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.阐明生物演化与气候变化、地质演化及其他历史演化模式之间的关联，是解析塑造生物多样性的核心过程的关键基础。将化石记录数据与分子系统发育学（molecular phylogenetics）相结合，是应对该科学挑战的极具前景的综合研究路径。首次分子分化定年分析（molecular divergence dating analysis，Zuckerkandl与Pauling，1962）基于对血红蛋白分子中氨基酸差异的量化分析，其替换速率的校准采用了来自教科书的不准确古生物年代估算值（例如：Dodson，1955）。自彼时起，分子序列数据量呈爆发式增长，为将分子分化定年方法应用于演化生物学的核心问题提供了愈发广阔的机遇。为充分利用这些契机，学界已开发且仍在持续研发愈发精密的分化定年方法。与之形成鲜明对比的是，针对分化定年分析中所使用的古生物学及相关地质数据开展批判性评估的研究却相对匮乏。由于缺乏基于化石设定校准点的严谨规范，分化定年结果的可信度受到了广泛质疑（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）。“错误的校准点会对分化定年研究产生负面影响”这一论断并无争议。目前已有通过后验方法（a posteriori methods）识别错误校准点的相关研究（例如：Near与Sanderson，2004；Near等，2005；Rutschman等，2007；Marshall，2008；Pyron，2010；Dornburg等，2011）。这类方法可使分子系统学家无需解读自身陌生且往往晦涩难懂的古生物学、地层学（stratigraphy）及地质年代学（geochronology）相关文献。多数后验方法会评估不同系统发育节点上的校准点之间的一致性，并剔除不一致的校准点。然而，化石校准点之间的一致性（或缺乏一致性）可能源于岩石记录中存在的时间或地理偏差。例如，若某一时间段内缺失岩石地层或化石，所有定年结果都可能被同等程度低估。在此类情况下，交叉验证可能会剔除那些更接近真实分化时间的校准点（Marshall，2008；Benton等，2009；Lee等，2009）。我们并不否认后验方法是评估校准点的有效手段，但古生物学数据真实性的先验（a priori）评估始终无可替代。