The timing and modes of macroevolutionary change: molecules, morphology, and simulations

项目概述：宏观进化可以使用现实世界（经验）数据和计算机模拟来研究。这个项目将通过结合这些方法来识别和研究深时间的进化模式。它将使用对真实世界系统发育数据的荟萃分析，结合定制的进化模拟软件来探索进化速度、物种和进化历史中的共同模式，以及它们背后的进化变化机制。方法：在已发表的形态学和分子（即总证据）系统发育研究中有大量可用的数据，可以重新用于研究宏观进化。这个博士学位的一个关键目标将是对这些进行荟萃分析。学生将收集系统发育数据，然后推导出具有不耦合形态和分子分支长度的贝叶斯系统发育（例如BEAST， MrBayes）。然后可以使用化石校准点来恢复速率，使用R语言和一系列统计方法来比较不同进化支的恢复速率。这将使学生能够识别和量化常见的模式。然后可以评估速率与潜在驱动因素之间的关系，例如环境变化、物种灭绝和进化新事物的出现。这些因素对发病率的不同影响（以及表型和基因型之间的差异）也将使用定制软件REvoSim进行研究。这是由监督小组成员（RJG和MDS）在过去八年中制定的，并于最近发表。例如，它已经展示了速率和物种形成事件之间潜在的令人兴奋的关系，以及这些事件与环境变化速率之间的关系。项目目标:1;使用结合分子和形态数据集（时间校准贝叶斯系统发生）的荟萃分析测量表型和基因型进化率，并描述这些速率的模式和相互关系。2. 测试与进化转变的相对时间有关的假设，如枝的起源、主要转变/新颖性和灭绝事件。3. 在REvoSim中进行进化模拟，以确定经验数据中观察到的模式在计算机上复制的参数，并研究修改这些参数的效果。

Project overview: Macroevolution can be studied using real-world (empirical) data, and computer simulations. This project will identify and investigate evolutionary patterns in deep time by combining these approaches. It will use a meta-analysis of real world phylogenetic data coupled with a custom-built evolutionary simulation software to explore evolutionary rates, common patterns in species and clade history, and the mechanisms of evolutionary change underlying them. Methods: There is a wealth of data available in the form of published morphological and molecular (i.e. total-evidence) phylogenetic studies that can be repurposed to investigate macroevolution. A key objective for this PhD will be to conduct a meta-analysis of these. The student will collect phylogenetic data, and then derive Bayesian phylogenies (using e.g. BEAST, MrBayes) with uncoupled morphological and molecular branch lengths. Fossil calibration points can then be used to recover rates, which will be compared across clades using the R language and a range of statistical approaches. This will allow the student to identify and quantify common patterns. The relationships between rates and potential drivers - such as periods of environmental change, extinctions, and the appearance of evolutionary novelties - can then be assessed. The differing impact of these factors on rates (and how this varies between the phenotype and genotype) will also be studied using the custom-built software REvoSim. This has been developed over the last eight years by members of the supervisory team (RJG and MDS) and was recently published. It already shows potentially exciting relationships between rates and speciation events, for example - and how these relate to the rate of environmental change.Project objectives: 1. Measure phenotypic and genotypic evolutionary rates using metaanalysis of combined molecular and morphological datasets (time-calibrated Bayesian phylogenies) and characterise the patterns and interrelationships of these rates. 2. Test hypotheses relating to the relative timing of evolutionary shifts such as the origin of clades, major transitions/novelties, and extinction events. 3. Conduct evolutionary simulations in REvoSim to identify the parameters under which patterns observed in the empirical data are replicated in silico, and study the effects of modifying these.