The Population Genetics of Divergence

分歧的群体遗传学

• 批准号: 7921487
• 负责人: Emanuel Hey
• 金额: $ 21.5万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7921487
• 关键词: Case Study; Confidence Intervals; DNA; Data Set; Genes; Genetic Drift; Human; Joints; Life; Markov Chains; Methods; Modeling; Pan Genus; Phylogenetic Analysis; Phylogeny; Population; Population Genetics; Population Sizes; Probability; Process; Relative (related person); Research; Research Project Grants; Sampling; Structure; Testing; base; density; novel strategies; simulation

DESCRIPTION (provided by applicant): Population divergence, including speciation and the origins of population structure, is the fundamental evolutionary process leading to the diversity of life. This research project will extend recent advances in a likelihood-based approach to divergence models. The new approach employs analytic integration over prior distributions of model parameters within a Markov chain Monte Carlo framework. The method leads to a joint probability density function, proportional to the likelihood that can be used for parameter estimation and log- likelihood ratio tests of nested demographic models. The new method will be adapted to general multi-population problems in divergence. Such problems have long been appreciated as requiring both a population genetic perspective and a phylogenetic perspective. The research plan outlines how these two can be brought together under a common MCMC simulation. This will be the first such method that does not assume a given phylogeny; that does not assume that gene flow has not occurred; and that makes no assumptions about the relative population sizes of sampled or ancestral populations. By providing estimates of the joint posterior density, proportional to the likelihood, the method will provide direct access to log-likelihood ratio tests and to likelihood-based confidence intervals. The approach will also be extended to problems in sample identification and DNA barcoding. These new methods will be applied to a case study of divergence among species and subspecies of Chimpanzee. The methods will also be applied to large multi-population multi-locus data sets from human populations.

描述（由申请人提供）：人口差异，包括物种形成和人口结构的起源，是导致生活多样性的基本进化过程。该研究项目将扩大基于可能性的差异模型方法的最新进展。新方法对马尔可夫链蒙特卡洛框架内模型参数的先前分布进行了分析集成。该方法导致联合概率密度函数，与可用于参数估计和对数可能性比率测试的可能性成正比。新方法将适应差异的一般多人群问题。长期以来，人们一直认为，这既需要人口遗传学的观点和系统发育的观点。该研究计划概述了如何在常见的MCMC模拟下聚集在一起。这将是第一种不假定给定系统发育的方法。那并不认为没有发生基因流。这对采样或祖先种群的相对种群规模没有任何假设。通过提供与可能性成正比的联合后密度密度的估计，该方法将直接访问对数可能性比率测试和基于可能性的置信区间。该方法还将扩展到样品识别和DNA条形码的问题。这些新方法将应用于黑猩猩物种和亚种之间差异的案例研究。该方法还将应用于人类人群中的大型多人群多核数据集。