Estimating Divergence Times and Evolutionary Rates

在生命之树上，有多少现存的物种，就有多少分歧。每一种分化都有一个日期（或者说，一个被认为比产生的谱系持续时间短的间隔），化石记录是关于这些日期的无价信息来源。虽然化石记录是不完整的，但它提供的信息可以用从DNA和蛋白质序列数据中提取的信息来补充。其基本思想是，如果序列来自近亲物种，则分子序列应该相似；如果序列来自远亲物种，则分子序列应该更加分化。在这个项目中，将开发统计程序来结合化石证据和来自现存生物体的DNA或蛋白质序列数据，以估计自共同祖先以来的时间。特别注意的是，DNA和蛋白质序列进化的时间顺序速率不是恒定的。这个项目的另一个目标将是推断出这些按时间顺序的进化速度随时间变化的模式。通过将分子进化随时间的时间变化速率划分为影响谱系中所有基因的部分和影响每个基因的部分，将会取得进展。还将强调改进对化石资料的处理和对基因复制的处理。在这个项目中开发的统计程序将有利于与生物多样性和分子生物学有关的广泛主题。生命之树上分支事件的日期分配为研究诸如物种形成和病原体或其他物种的传播等过程提供了一个框架。估计分子进化的时间顺序速率以及这些速率如何随时间变化的能力也有多种应用，包括蛋白质功能和功能创新的研究，以及评估自然选择和遗传漂变对进化的重要性。在研究过程中，将为一名研究生提供现代计算生物学方面的培训，首席研究员杰弗里·索恩博士和该研究生将前往日本，与东京大学著名统计学家岸野博久博士一起工作。作为项目的一部分开发的源代码是免费提供的，就像以前索恩博士开发的发散时间软件一样。

There are almost as many divergences on the tree of life as there are extant species. Each of these divergences has a date (or, an interval presumed shorter in duration than the resultant lineages), and the fossil record is a priceless source of information about these dates. Although the fossil record is incomplete, the information that it provides can be supplemented with information extracted from DNA and protein sequence data. The basic idea is that molecular sequences should be similar if sequences are derived from closely related species and should be more diverged if the sequences come from more distantly related species. In this project, statistical procedures will be developed for combining fossil evidence and DNA or protein sequence data from extant organisms in order to estimate time since common ancestry. Special attention will be given to the fact that chronological rates of DNA and protein sequence evolution are not constant. Another goal of this project will be to infer the pattern by which these chronological rates of evolution change over time. Progress will be made by partitioning the change over time of chronological rates of molecular evolution into a portion that affects all genes in a lineage and a portion that affects each individual gene. Improved treatment of fossil data and handling of gene duplications will also be emphasized. The statistical procedures to be developed in this project will benefit a wide range of topics related to both biodiversity and molecular biology. The assignment of dates to branching events on the tree of life provides a framework for studying processes such as speciation and the dispersal of pathogens or other species. The ability to estimate chronological rates of molecular evolution and how these rates change over time also has diverse applications that include the study of protein function and functional innovation as well as the assessment of the importance to evolution of natural selection and genetic drift. Training for a graduate student in modern computational biology will be provided during the course of the research, and both the principal investigator, Dr. Jeffrey Thorne, and the graduate student will travel to Japan to work with the eminent statistician Dr. Hirohisa Kishino at the University of Tokyo. Source code developed as part of the project is made freely available, as has been the case with previous divergence-time software developed by Dr. Thorne.