Rocks for clocks

尽管化石记录传统上为进化史提供了时间尺度，但近年来这种作用已被分子钟完全篡夺。分子时钟建立在几个看似简单的假设上：(I)随机复制错误导致的基因序列中的突变；(Ii)不同生物的基因差异量是自它们共享祖先以来的时间的函数；(Iii)如果可以根据化石记录确定祖先的年龄，也可以确定突变的累积速度；(Iv)通过外推，可以使用该速度来确定其他谱系之间进化分歧的时间。然而，化石记录提供了唯一可行的方法来校准分子时钟与时间，因此，如果分子时钟分析要成为建立进化时间表的有效和可靠的手段，就必须克服化石估计仅近似于谱系之间进化分裂的时间这一事实。令人惊讶的是，直到最近，化石校准的问题一直被完全忽视。然而，两个主要的分子时钟软件包现在提供了一种表示校准中的不确定性的方法，因为先前的假设表现为随时间变化的概率包络，并且可能适合于单独的校准。然而，由于缺乏可作为依据的证据，它们很少得到实施。该提案的目的是根据唯一适当的数据--关于控制化石地层分布的偏差的知识--探索这种先验概率的编码化。一般认为，化石是随机分布在岩层中的。然而，人们早就知道，化石的分布受到代表化石生物体所在沉积物的岩石分布的严格控制。事实上，化石的分布可以从与它们相关的岩石的分布中预测出来。因此，有可能区分缺乏具有谱系代表性的化石，因为(A)没有合适的岩石序列可供采样，(B)没有获得合适的化石条件(因为近亲也没有化石)，以及(C)谱系尚未进化--从这一点可以为谱系分化建立最大日期限制。在建立了最小(所述谱系的最古老化石记录)和最大约束的情况下，还可以建立一个中间概率密度，该概率密度描述了谱系分歧的概率如何随可用于采样的合适岩石的可获得性而变化。我们的最终目标是在化石分布受沉积环境细微变化控制的情况下建立和实施这种先验。然而，在这项提议中，我们的目标是探索在对一个广泛的进化事件--动物主要谱系的建立，也称为寒武纪爆发--的分子时钟分析中，这种先验概率的编纂和实施。之所以选择这个例子，是因为先验可以简单地建立在海相岩石在寒武纪-显生宙期间面积范围的变化上，在这种变化中，这些谱系彼此分叉。大多数数据已经就位-显生界的地质数据已经收集，但我们将收集低温生代和埃迪卡拉纪的数据，基于这些原始数据的先验数据与更简单的替代数据的性能将被确定。该项目还将作为一项培训活动，这位古生物学家将接受培训，在项目的最早阶段进行分子钟分析，他将把这些技能传授给布里斯托尔的其他古生物学工作人员和学生，为他们提供奇异的技能，使他们能够重新解决古老的古生物学问题。

Though the fossil record has traditionally provided the timescale for evolutionary history, this role has been usurped completely in recent years by the molecular clock. The molecular clock rests on a few deceptively simple assumptions: (i) mutations accrue within genetic sequences as a result of random copy errors, (ii) the amount of differences in genes of different organisms is a function of the time since they shared an ancestor, (iii) if the age of that ancestor can be determined from the fossil record, the rate at which mutations have accrued can also be determined and, by extrapolation, (iv) the rate can be used to date the times of evolutionary divergence between other lineages. However, the fossil record provides the only viable means of calibrating the molecular clock to time and, thus, the fact that fossil estimates only approximate the timing of evolutionary splits between lineages must be overcome if molecular clock analyses are to be an effective and reliable means of establishing an evolutionary timescale. Surprisingly, the problem of fossil calibrations has been completely ignored until recently. However, the two main molecular clock software packages now provide a means of expressing the uncertainty in calibrations as prior assumptions manifest as probability envelopes that vary with time and may be adapted to individual calibrations. However, they have rarely been implemented for want of evidence on which to base them. The aim of the proposal is to explore the codification of such prior probabilities based on the only appropriate data - knowledge of the biases that control the stratigraphic distribution of fossils. It is generally thought that fossils are randomly distributed within rock sequences. However, it has long been known that the distribution of fossils is tightly controlled by the distribution of rocks representative of the sediments in which the fossil organisms lived. Indeed, the distribution of fossils can be predicted from the distribution of rocks to which they are associated. Thus, it is possible to distinguish between an absence of lineage-representative fossils because (a) there are no suitable rock sequences to sample, (b) suitable fossilization conditions did not obtain (because relatives are also not fossilized), and (c) the lineage had not yet evolved - from which a maximum date constraint may be established for lineage divergence. With minimum (oldest fossil record of the lineage in question) and maximum constraints established, an intervening probability density may also be established that describes how the probability of lineage divergence varies with the availability of suitable rock for sampling. It is our ultimate aim to establish and implement such priors in circumstances where fossil distributions are controlled by subtle variations in sedimentary environments. However, in this proposal we aim to explore the codification and implementation of such prior probabilities in a molecular clock analysis of a broad scale evolutionary event - the establishment of the principal lineages of animals, also known as the Cambrian Explosion. This example is chosen because the priors may be established simply, on variation in the areal extent of marine rock through the Cryogenian-Phanerozoic interval in which these lineages diverged one from another. Most of the data are in place - geological data have been gathered for the Phanerozoic, but we will gather data for the Cryogenian and Ediacaran, and the performance of priors based on these raw data, versus simpler proxies, will be determined. The project will also serve as a training exercise in which the researcher, a palaeontologist, will be trained to perform the molecular clock analyses during the earliest stages of the project, and he will transfer these skills to the other palaeontological staff and students in Bristol, providing them with exotic skills that will allow them to address age-old palaeontological problems anew.