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 paleontological age estimates from textbooks (e.g., Dodson 1960). 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 (e.g., Shaul and Graur 2002; Brochu et al. 2004; Graur and Martin 2004; Hedges and Kumar 2004; Reisz and Muller 2004a, 2004b; Theodor 2004; van Tuinen and Hadly 2004a, 2004b; 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; Rutschmann et al. 2007; Marshall 2008; Pyron 2010; Dornburg et al. 2011). 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. Incorrect calibrations, those based upon fossils that are phylogenetically misplaced or assigned incorrect ages, clearly introduce error into an analysis. Consequently, thorough and explicit justification of both phylogenetic and chronologic age assessments is necessary for all fossils used for calibration. Such explicit justifications will help to ensure that divergence dating studies are based on the best available data. Unfortunately, the majority of previously published calibrations lack explicit explanations and justifications of the age and phylogenetic position of the key fossils. In the absence of explicit justifications, it is difficult to distinguish between correct and incorrect calibrations, and it becomes difficult to reevaluate previous claims in light of new data. Paleontology is a dynamic science, with new data and perspectives constantly emerging as a result of new discoveries (see Kimura 2010 for a recent case where the age of the earliest known record of a clade was more than doubled). Calibrations based upon the best available evidence at a given time can become inappropriate as the discovery of new specimens, new phylogenetic analyses, and ongoing stratigraphic and geochronologic revisions refine our understanding of the fossil record. Our primary goals in this paper are to establish the best practices for justifying fossils used for the temporal calibration of molecular phylogenies. Our examples derive mainly, but not exclusively, from the vertebrate fossil record. We hope that our recommendations will lead to more credible calibrations and, as a result, more reliable divergence dates throughout the tree of life. A secondary goal is to help the community (researchers, editors, and reviewers) who might be unfamiliar with fossils to understand and overcome the challenges associated with using paleontological data. In order to accomplish these goals, we present a specimen-based protocol for selecting and documenting relevant fossils and discuss future directions for evaluating and utilizing phylogenetic and temporal data from the fossil record. We likewise encourage biologists relying on nonfossil calibrations for molecular divergence estimates (e.g., ages of island or mountain range formations, continental drift, and biomarkers) to develop their own set of rigorous guidelines so that their calibrations may also be evaluated in a systematic way.

中文翻译：

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证明化石校准合理性的最佳实践

我们将生物进化与气候变化、地质进化和其他历史模式相关联的能力对于理解塑造生物多样性的过程至关重要。将来自化石记录的数据与分子系统发生学相结合代表了一种令人兴奋的合成方法来应对这一挑战。第一次分子差异定年分析（Zuckerkandl 和 Pauling 1962）基于血红蛋白分子中氨基酸差异的测量，使用教科书（例如，Dodson 1960）中的古生物学年龄估计确定（校准）替代率。从那时起，分子序列数据的数量急剧增加，为将分子发散方法应用于进化生物学中的基本问题提供了越来越多的机会。为了抓住这些机会，越来越复杂的背离测年方法已经并将继续被开发。相比之下，相对而言，很少有人关注批判性地评估用于分歧定年分析的古生物学和相关地质数据。缺乏根据化石分配校准的严格协议引发了关于发散定年结果可信度的严重问题（例如，Shaul 和 Graur 2002；Brochu 等人 2004；Graur 和 Martin 2004；Hedges 和 Kumar 2004；Reisz 和 Muller 2004a， 2004b；西奥多 2004；van Tuinen 和 Hadly 2004a，2004b；van Tuinen 等人 2004；Benton 和 Donoghue 2007；Donoghue 和 Benton 2007；Parham 和 Irmis 2008；Ksepka 2009 2009 年 1. 不正确的校准将对分歧测年研究产生负面影响的断言是没有争议的。可以尝试通过使用后验方法来识别不正确的校准（例如，Near 和 Sanderson 2004；Near 等人 2005；Rutschmann 等人 2007；Marshall 2008；Pyron 2010；Dornburg 等人 2011）。我们不否认后验方法是评估校准的有用手段，但不能替代对古生物学数据准确性的先验评估。不正确的校准，即基于系统发育错位或分配不正确年龄的化石，显然会在分析中引入错误。因此，对于用于校准的所有化石，系统发育和年代学年龄评估的彻底和明确的理由是必要的。这种明确的理由将有助于确保分歧测年研究基于最佳可用数据。很遗憾，大多数先前发表的校准缺乏对关键化石的年龄和系统发育位置的明确解释和理由。在没有明确理由的情况下，很难区分正确和不正确的校准，也很难根据新数据重新评估以前的声明。古生物学是一门动态的科学，随着新发现的不断涌现，新的数据和观点不断涌现（见木村 2010 年最近的一个案例，其中已知最早的进化枝记录的年龄翻了一番多）。随着新标本的发现、新的系统发育分析以及正在进行的地层学和地质年代学修订完善了我们对化石记录的理解，基于给定时间的最佳可用证据进行的校准可能变得不合适。我们在本文中的主要目标是建立证明用于分子系统发育时间校准的化石的最佳实践。我们的例子主要但不完全来自脊椎动物化石记录。我们希望我们的建议将导致更可靠的校准，从而在整个生命之树中获得更可靠的分歧日期。第二个目标是帮助可能不熟悉化石的社区（研究人员、编辑和评论员）理解和克服与使用古生物学数据相关的挑战。为了实现这些目标，我们提出了一个基于样本的协议，用于选择和记录相关化石，并讨论评估和利用来自化石记录的系统发育和时间数据的未来方向。