Rocks for clocks

钟表用岩石

• 批准号: NE/G009600/1
• 负责人: Philip Donoghue
• 金额: $ 6.18万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FG009600%2F1
• 关键词: Rocks; clocks

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.

尽管化石记录传统上为进化史提供了时间尺度，但近年来，这一角色已被分子钟完全取代。分子钟建立在几个看似简单的假设之上：(i)基因序列中的突变是随机复制错误的结果，（ii）不同生物基因差异的数量是它们共享祖先的时间函数，（iii）如果祖先的年龄可以从化石记录中确定，那么突变积累的速率也可以确定，通过外推，（iv）速率可以用来确定其他谱系之间进化分歧的时间。然而，化石记录提供了校准分子钟时间的唯一可行方法，因此，如果分子钟分析要成为建立进化时间标度的有效和可靠的方法，化石估计只能近似于谱系之间进化分裂的时间这一事实必须克服。令人惊讶的是，化石校准的问题直到最近才被完全忽视。然而，两个主要的分子钟软件包现在提供了一种方法来表达校准中的不确定性，因为先前的假设表现为随时间变化的概率信封，并且可以适应个别校准。然而，由于缺乏证据作为基础，它们很少得到执行。该提案的目的是探索基于唯一适当的数据-控制化石地层分布的偏差知识的这种先验概率的编纂。一般认为化石是随机分布在岩石层序中的。然而，人们早就知道，化石的分布受到化石生物所生活的代表沉积物的岩石分布的严格控制。的确，化石的分布可以通过与之相联系的岩石的分布来预测。因此，有可能区分谱系代表性化石的缺失，因为(a)没有合适的岩石序列进行取样，(b)没有获得合适的石化条件（因为亲属也没有石化），以及(c)谱系尚未进化——由此可以建立谱系分化的最大日期约束。在确定了最小约束条件（有关谱系最古老的化石记录）和最大约束条件后，还可以建立一个中间概率密度，该密度描述谱系分化的概率如何随适合取样的岩石的可用性而变化。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，在这个提议中，我们的目标是在分子钟分析中探索这种先验概率的编纂和实现，这是一个大规模的进化事件——动物主要谱系的建立，也被称为寒武纪大爆发。之所以选择这个例子，是因为这些先例可以简单地建立在海相岩石面积范围的变化上，通过这些谱系相互分化的低温-显生宙区间。大部分数据都已到位——显生宙的地质数据已经收集完毕，但我们将收集低温纪和埃迪卡拉纪的数据，并将根据这些原始数据与更简单的代理来确定先验的性能。该项目还将作为一项培训活动，作为古生物学家的研究人员将接受培训，在项目的最初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教职员工和学生，为他们提供新奇的技能，使他们能够重新解决古老的古生物学问题。

项目成果

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales.

• DOI: 10.1016/j.cub.2015.09.066
• 发表时间: 2015-11-16
• 期刊: Current biology : CB
• 作者: dos Reis M;Thawornwattana Y;Angelis K;Telford MJ;Donoghue PC;Yang Z
• 通讯作者: Yang Z

DO CLADISTIC AND MORPHOMETRIC DATA CAPTURE COMMON PATTERNS OF MORPHOLOGICAL DISPARITY?

• DOI: 10.1111/pala.12159
• 发表时间: 2015-05-01
• 期刊: PALAEONTOLOGY
• 影响因子: 2.6
• 作者: Hetherington, Alexander J.;Sherratt, Emma;Donoghue, Philip C. J.
• 通讯作者: Donoghue, Philip C. J.

Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils.

• DOI: 10.1111/pala.12178
• 发表时间: 2015-09
• 期刊: Palaeontology
• 影响因子: 2.6
• 作者: Schirrmeister BE;Gugger M;Donoghue PC
• 通讯作者: Donoghue PC

A DIVERGENCE DATING ANALYSIS OF TURTLES USING FOSSIL CALIBRATIONS: AN EXAMPLE OF BEST PRACTICES

• DOI: 10.1666/12-149
• 发表时间: 2013-07-01
• 期刊: JOURNAL OF PALEONTOLOGY
• 影响因子: 1.4
• 作者: Joyce, Walter G.;Parham, James F.;Donoghue, Philip C. J.
• 通讯作者: Donoghue, Philip C. J.