进化速率概念的提出：
Zuckerkand and Pauling
molecular clock
1960s,许多研究团队发现了，不同物种间蛋白替换的速率十分一致。这个假设的单一的进化速率就称为“分子钟”，并且生物学家意识到这是一个衡量分化时间的标尺。
但是随着近五十年测序技术和计算工具的飞跃，生物学家发现进化速率在生命之树的不同部分差距很大。
The term ‘molecular clock’ is now used more broadly to refer to a suite of methods and models that assess how rates of genetic evolution vary across the tree of life, and use this information to put an absolute timescale on this tree.
现在分子钟的概念更广了，它指的是一系列用于评估不同进化速率的方法和模型，以及运用这些信息推算生命之树的绝对时间。
一，进化速率的不同
Modern molecular clocks can handle various forms of evolutionary rate heterogeneity. Rates can vary across different parts of the genome (site effects), across taxa (lineage effects), and across time (here termed ‘epoch effects’).
现代分子钟可以处理各种形式的进化速率不一致。不同的基因组位置，不同的分类群和不同的时间都会存在进化速率的不同。
For example, rodents have higher rates of genetic change than do other mammals, partly due to their short generation times.
啮齿动物比其他哺乳动物进化速率快，部分是由于他们的世代时间短。
Likewise, parasitic plants evolve more rapidly than their free-living relatives.
同样的，寄生植物要比它们自由生活的近亲进化的要快。
Selection might be relaxed on particular genes in particular taxa and thus lead to rapid molecular evolution.
对于特定物种的特定基因，选择压力可能比较松，从而导致它的进化较快。
二，分子钟的校正
Genetic divergences alone, even when analysed using the most sophisticated molecular clock models, are only able to provide a relative timescale.
光靠遗传差异本身，就算依靠最复杂的分子钟模型，也只能给出相对的时间表。
The molecular clock needs to be calibrated in order to translate these relative dates into absolute ones. Calibrations are typically derived from the fossil record and biogeographic information.
生物钟需要校正，来把相对时间转化为绝对时间。校正一般是通过化石记录，现在也有利用生物地理信息的方法。
三，Evolutionary timescales 进化时间表
However, a persistent pattern is that the molecular dates of evolutionary events are often still substantially older than suggested by the fossil record.
通过分子钟对分化时间的推断对解释很多进化问题至关重要，但是一般分子钟推算的进化事件的时间总是比化石记录的时间要久远。
四，Genomic clocks 基因组钟
Our ability to collect vast amounts of genetic data is rapidly outstripping our ability to rigorously analyse them, and molecular clock analyses are no exception.
我们收集大量基因数据的能力已经快速超过了我们严格分析它们的能力，分子钟也不是例外。哈哈哈，这句话。
For example, it is possible to find groups of genes that have been subject to the same lineage effects, meaning that they have evolved according to the same molecular clock.
基因数据及物种数目的增多，分子钟模型也变得复杂，非常耗费计算资源。
我们可以只挑选经历相同种系效应的一组基因，这意味着他们是按照相同分子钟进化的。
Increasing the amount of genetic data does little to mitigate the major remaining sources of error — the model of rate variation and the calibrations — which are the other two critical components of molecular clock inferences.
增加基因数据数量，对于减轻变异速率模型和校正所引起的错误，所起的作用很小。
这种情况需要改变变异速率模型和校正方法。
We are reaching the point where increasing the amount of molecular data brings a declining benefit to our estimates of evolutionary timescales. Instead, more room for improvement might lie in developing better models of rate variation and refining our knowledge and use of calibrations.
我们已经到达了一个增加数据数量对进化时间估计效益降低的节点。相反，在开发更好的变异率模型和改善我们对校正的知识和利用方面还有很大空间。
