Estimating Divergence Times and Evolutionary Rates

估计分歧时间和进化速率

• 批准号: 0445180
• 负责人: Jeffrey Thorne
• 金额: --
• 依托单位: North Carolina State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-04-01 至 2009-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0445180&HistoricalAwards=false
• 关键词: Estimating; Divergence; Times; Evolutionary; Rates

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.

生命之树上的分歧几乎与现存物种一样多。 这些分歧中的每一个都有一个日期（或者，假定持续时间比由此产生的谱系更短的间隔），而化石记录是有关这些日期的无价信息来源。 尽管化石记录不完整，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进行补充。 基本思想是，如果序列来自密切相关的物种，则分子序列应该相似；如果序列来自更远近的物种，则分子序列应该更加不同。 在该项目中，将开发统计程序，将化石证据与现存生物体的 DNA 或蛋白质序列数据相结合，以估计自共同祖先以来的时间。 我们将特别关注 DNA 和蛋白质序列进化的时间速率并不是恒定的这一事实。 该项目的另一个目标是推断这些进化速度随时间变化的模式。 通过将分子进化的时间速率随时间的变化划分为影响谱系中所有基因的部分和影响每个单独基因的部分，将取得进展。 还将强调改进化石数据的处理和基因重复的处理。 该项目将开发的统计程序将有利于与生物多样性和分子生物学相关的广泛主题。 生命树上分支事件的日期分配为研究物种形成和病原体或其他物种的传播等过程提供了框架。 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具有多种应用，包括研究蛋白质功能和功能创新以及评估自然选择和遗传漂变进化的重要性。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 Jeffrey Thorne 博士和该研究生都将前往日本与东京大学著名统计学家 Hirohisa Kishino 博士一起工作。作为该项目的一部分开发的源代码是免费提供的，就像索恩博士之前开发的分歧时间软件的情况一样。