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Improving Bayesian methods for estimating divergence times integrating genomic and trait data

改进贝叶斯方法来估计整合基因组和性状数据的分歧时间

基本信息

批准号：
BB/N000609/1
负责人：
Ziheng Yang
金额：
$ 48.31万
依托单位：
University College London
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2016
资助国家：
英国
起止时间：
2016 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FN000609%2F1
关键词：
Improving Bayesian methods estimating divergence

项目摘要

After one species splits into two, their genes and genomes will evolve independently. If the rate of evolution is constant over time, the genetic differences between species will accumulate at a fixed pace, proportional to the time of species separation. Thus molecules can serve as a clock, keeping time of species separation by the accumulated changes. If fossil records or geological events can be used to assign an absolute geological time to a species divergence event on the evolutionary tree, one can convert all calculated genetic distances into absolute geological times. This rationale for molecular clock dating has recently been extended to deal with variable evolutionary rate over time in the so-called relaxed-clock models. For fast-evolving viral DNA, the different sampling times of the viral sequences allows us to similarly calibrate the molecular and to obtain estimates of the absolute divergence times and evolutionary rates. In this project, we will develop statistical models of trait evolution, which will be used to analyse morphological trait data for both living and extinct species to generate fossil calibrations, which are crucially important to molecular dating analysis. Such models of trait evolution will also allow us to study the correlation between viral molecular sequence evolution and viral genotypes such as antigenic drift. We will apply the new methods to analyse real datasets to date major divergence events in the tree of life, such as the divergences of the human and the apes, the primates, the animals, and the flowering plants.

一个物种分裂成两个物种后，它们的基因和基因组将独立进化。如果进化的速度随着时间的推移是恒定的，物种之间的遗传差异将以固定的速度积累，与物种分离的时间成正比。因此，分子可以作为一个时钟，通过积累的变化来保持物种分离的时间。如果化石记录或地质事件可以用来为进化树上的物种分化事件指定一个绝对的地质时间，那么人们可以将所有计算出的遗传距离转换为绝对的地质时间。这种分子时钟定年的基本原理最近被扩展到处理所谓的松弛时钟模型中随时间变化的进化速率。对于快速进化的病毒DNA，病毒序列的不同采样时间使我们能够类似地校准分子，并获得绝对分化时间和进化速率的估计。在这个项目中，我们将开发性状进化的统计模型，该模型将用于分析现存和灭绝物种的形态性状数据，以生成化石校准，这对分子定年分析至关重要。这种性状进化模型也将使我们能够研究病毒分子序列进化与病毒基因型（如抗原漂移）之间的相关性。我们将应用新的方法来分析真实的数据集，以确定生命之树上的主要分化事件，例如人类与猿类、灵长类动物、动物和开花植物的分化。