進化速率概念的提出：

Zuckerkand and Pauling

molecular clock

1960s,許多研究團隊發(fā)現(xiàn)了，不同物種間蛋白替換的速率十分一致。這個假設(shè)的單一的進化速率就稱為“分子鐘”，并且生物學(xué)家意識到這是一個衡量分化時間的標(biāo)尺。

但是隨著近五十年測序技術(shù)和計算工具的飛躍，生物學(xué)家發(fā)現(xiàn)進化速率在生命之樹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.?

現(xiàn)在分子鐘的概念更廣了，它指的是一系列用于評估不同進化速率的方法和模型，以及運用這些信息推算生命之樹的絕對時間。

一，進化速率的不同

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’).

現(xiàn)代分子鐘可以處理各種形式的進化速率不一致。不同的基因組位置，不同的分類群和不同的時間都會存在進化速率的不同。

For example, rodents have higher rates of genetic change than do other mammals, partly due to their short generation times.

嚙齒動物比其他哺乳動物進化速率快，部分是由于他們的世代時間短。

Likewise, parasitic plants evolve more rapidly than their free-living relatives.

同樣的，寄生植物要比它們自由生活的近親進化的要快。

Selection might be relaxed on particular genes in particular taxa and thus lead to rapid molecular evolution.?

對于特定物種的特定基因，選擇壓力可能比較松，從而導(dǎo)致它的進化較快。

二，分子鐘的校正

Genetic divergences alone, even when analysed using the most sophisticated molecular clock models, are only able to provide a relative timescale.?

光靠遺傳差異本身，就算依靠最復(fù)雜的分子鐘模型，也只能給出相對的時間表。

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.

生物鐘需要校正，來把相對時間轉(zhuǎn)化為絕對時間。校正一般是通過化石記錄，現(xiàn)在也有利用生物地理信息的方法。

三，Evolutionary timescales 進化時間表

However, a persistent pattern is that the molecular dates of evolutionary events are often still substantially older than suggested by the fossil record.

通過分子鐘對分化時間的推斷對解釋很多進化問題至關(guān)重要，但是一般分子鐘推算的進化事件的時間總是比化石記錄的時間要久遠。

四，Genomic clocks 基因組鐘

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.

我們收集大量基因數(shù)據(jù)的能力已經(jīng)快速超過了我們嚴(yán)格分析它們的能力，分子鐘也不是例外。哈哈哈，這句話。

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.?

基因數(shù)據(jù)及物種數(shù)目的增多，分子鐘模型也變得復(fù)雜，非常耗費計算資源。

我們可以只挑選經(jīng)歷相同種系效應(yīng)的一組基因，這意味著他們是按照相同分子鐘進化的。

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.

增加基因數(shù)據(jù)數(shù)量，對于減輕變異速率模型和校正所引起的錯誤，所起的作用很小。

這種情況需要改變變異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.?

我們已經(jīng)到達了一個增加數(shù)據(jù)數(shù)量對進化時間估計效益降低的節(jié)點。相反，在開發(fā)更好的變異率模型和改善我們對校正的知識和利用方面還有很大空間。