Forest Félix
Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
Ann Bot. 2009 Oct;104(5):789-94. doi: 10.1093/aob/mcp192. Epub 2009 Aug 8.
Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.
The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.
自20世纪60年代分子钟假说提出以来，分子年代测定越来越受到关注。分子年代测定为系统发育树中的分歧事件提供了详细的时间框架，使得各种进化问题得以解决。分子钟假说的关键方面，即两个物种之间DNA或蛋白质序列的差异与它们分化后经过的时间成正比，很快就被证明是站不住脚的。人们提出了其他方法来考虑谱系间的速率异质性，但直到最近，将相对时间转换为绝对年龄的校准过程很少受到关注。现在已经提出了新的方法来解决与系统发育树校准相关的潜在误差来源，特别是那些涉及化石记录使用的误差来源。
本文主要关注在校准过程中使用化石记录作为独立信息来源；还讨论了其他校准信息来源。确定了化石校准特别容易出错的方面，如化石年代测定、化石在系统发育中的位置以及化石记录的不完整性。讨论了为解决这些潜在误差来源中的一个或多个而提出的方法（例如化石交叉验证、校准点的先验分布以及化石记录的置信区间）。总之，化石记录仍然是校准系统发育树最可靠的信息来源，尽管必须考虑相关的假设和潜在偏差。
