The Population Genetics of Divergence

分歧的群体遗传学

• 批准号: 8698900
• 负责人: Emanuel Hey
• 金额: $ 23.34万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 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 2017-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8698900
• 关键词: Address; Americas; Budgets; Case Study; Cell Line; Child; Chromosome Mapping; Cities; Clinical Research; Clinical Trials; Complex; Confidence Intervals; DNA; Data; Data Set; Denmark; Development; Enrollment; Event; Evolution; Face; Genealogy; General Population; Genes; Genetic; Genetic Drift; Human; Human Resources; Human Subject Research; Individual; Instruction; Joints; Last Name; Leadership; Letters; Life; Linkage Disequilibrium; Literature; Manuscripts; Markov Chains; Methods; Minority; Modeling; Monitor; Monte Carlo Method; Names; New Brunswick; New Jersey; Pan Genus; Pattern; Phase; Phylogenetic Analysis; Phylogeny; Population; Population Genetics; Population Group; Population Sizes; Principal Investigator; Printing; Probability; Process; Progress Reports; Protocols documentation; Publications; Publishing; Recording of previous events; Relative (related person); Research; Research Design; Research Methodology; Research Personnel; Research Project Grants; Resource Sharing; Resources; Role; Safety; Sampling; Space Simulation; Structure; Testing; Trees; Uncertainty; Universities; Update; Vertebrates; Woman; base; density; human embryonic stem cell; human subject protection; improved; indexing; joint function; novel strategies; performance site; programs; research study; simulation; tool

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 ditributions 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 acces 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. PERFORMANCE SITE(S) (organization, city, state) Rutgers, the State University of New Jersy, New Brunswick New Jersey, USA The University of Copenhagen, Copenhagen, Denmark. PHS 398 (Rev. 04/06) Page 2 Form Page 2 Principal Investigator/Program Director (Last, First, Middle): Hey, Emanuel B. KEY PERSONNEL. See instructions. Use continuation pages as needed to provide the required information in the format shown below. Start with Principal Investigator(s). List all other key personnel in alphabetical order, last name first. Name eRA Commons User Name Organization Role on Project Hey, Emanuel B. EMANUELHEY Rutgers University PI Nielsen, Rasmus Univ. of Copenhagen Co-Pi OTHER SIGNIFICANT CONTRIBUTORS Name Organization Role on Project Human Embryonic Stem Cells [x] No Q yes If the proposed project Involves human embryonic stem cells, list below the registration number of the specific cell line(s) from the following list: http://stemcells.nih.qov/reqistrv/index.asp. Use continuation pages as needed. Ifaspecificlinecannotbereferencedatthistime,includeastatementthatonefromtheRegistrywillbeused. Cell Line PHS 398 (Rev. 04/06) Page 3 Form Page 2-continued Number the following pages consecutively throughout the application. Do not use suffixes such as 4a, 4b. Principal Investigator/Program Director (Last, First, Middle): Hey, Emanuel B The name of the principal investigator/program director must be provided at the top of each printed page and each continuation page. RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page 1 Description, Performance Sites, Key Personnel, Other Significant Contributors, and Human Embryonic Stem Cells Table of Contents Detailed Budget for Initial Budget Period (or Modular Budget) Budget for Entire Proposed Period of Support (not applicable with Modular Budget) na Budgets Pertaining to Consortium/Contractual Arrangements (not applicable with Modular Budget) na Biographical Sketch - Principal Investigator/Program Director (Not to exceed four pages) Other Biographical Sketches (Not to exceed four pages for each - Seeinstructions) Resources 12 Research Plan, 13 Introduction to Revlsed/Resubmission Application (Not to exceed 3 pages.). 13 Introduction to Supplemental/Revision Application (Not to exceed one page.) na A. Specific Aims Jl B. Background and Significance 17 C. Preliminary Studies/Progress Report (Items A-D: not to exceed 25 pages). 22 D. Research Design and Methods 34 E. Human Subjects Research 41 Protection of Human Subjects (Required if Item 4 on the Face Page is marked "Yes") na Data and Safety Monitoring Plan (Required if Item 4 on the Face Page is marked "Yes" and a Phase I, II, or III clinical trial is proposed) na Inclusion of Women and Minorities (Required if Item 4 on the Face Page is marked "Yes" and is Clinical Research) na Targeted/Planned Enrollment Table (for new and continuing clinical research studies) na Inclusion of Children (Required if Item 4 on the Face Page is marked "Yes") na F. Vertebrate Animals na G. Select Agent Research na H. Literature Cited 41 I, Multiple PI Leadership Plan 46 J. Consortium/Contractual Arrangements 46 K. Resource Sharing na L. Letters of Support (e.g., Consultants) na Checklist. 47 Check if Appendix(Fivecollatedsets.NopagenumberingnecessaryforAppendix.) Appendix is Included Number of publications and manuscripts accepted for publication (not to exceed 10) Other items (list): PHS 398 (Rev. 04/06) Page 4 Form Page 3

人口差异，包括物种形成和人口结构的起源，是基本 进化过程导致生活的多样性。该研究项目将扩大最新进展 基于可能性分歧模型的方法。新方法对先验进行了分析集成 马尔可夫链蒙特卡洛框架内模型参数的占用。该方法导致关节 概率密度函数与可能性成正比，可用于参数估计和log- 嵌套人口模型的似然比测试。 新方法将适应差异的一般多人群问题。这样的问题有 长期以来，人们被认为需要人口遗传学的观点和系统发育的观点。这 研究计划概述了如何在常见的MCMC模拟下聚集在一起。这会 是第一种不假定给定系统发育的方法；那并不认为基因流没有 发生；这对采样或祖先的相对种群大小没有任何假设 人群。通过提供与可能性成正比的联合后密度的估计，该方法 将提供直接的与对数似然比测试和基于似然的置信区间的配件。 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对物种和亚种之间差异的案例研究 黑猩猩。该方法还将应用于人类的大型多人群多核数据集 人群。 绩效网站（组织，城市，州） 新泽西州立大学新泽西州立大学罗格斯，美国新泽西州新泽西州 哥本哈根大学哥本哈根，丹麦。 PHS 398（修订版04/06）第2页表格页2 首席研究员/计划主任（最后，第一，中间）：嘿，伊曼纽尔·B。 关键人员。请参阅说明。根据需要使用延续页面，以下面显示的格式提供所需的信息。 从首席研究员开始。按字母顺序列出所有其他关键人员，首先姓氏。 名称ERA CONSONS用户名组织在项目中的角色 嘿，Emanuel B. Emanuelhey Rutgers University Pi 尼尔森，拉斯穆斯大学。哥本哈根Co-Pi 其他重要的贡献者 姓名组织角色 人类胚胎干细胞[x]否q是 如果所提出的项目涉及人类胚胎干细胞，请从以下列表中列出特定细胞系的注册数： http：//stemcells.nih.qov/reqistrv/index.asp。根据需要使用延续页面。 ifaspecificlinecannotbereedcretedatthistime，包括eastatementthatonefromtheregistrywillbeused。 细胞系 PHS 398（修订版04/06）第3页表格第2页。 在整个过程中连续编号以下页面 应用程序。请勿使用4A，4B等后缀。 首席调查员/计划总监（最后，第一，中间）：嘿，伊曼纽尔B 必须在每个印刷页面的顶部和每个延续页面的顶部提供主要调查员/计划主管的名称。 研究赠款 目录 页码 面部第1页 描述，绩效站点，关键人员，其他重要贡献者和人类 胚胎干细胞 目录 初始预算期（或模块化预算）的详细预算 整个建议的支持期预算（不适用于模块化预算）NA 与财团/合同安排有关的预算（不适用于模块化预算）NA 传记素描 - 首席研究员/计划总监（不超过四页） 其他传记草图（每个人不超过四页 - see Instructions） 资源12 研究计划，13 介绍Revlsed/Repubmission申请（不超过3页）。 13 补充/修订申请简介（不超过一页。）NA A.特定目标JL B.背景和意义17 C.初步研究/进度报告（项目A-D：不超过25页）。 22 D.研究设计和方法34 E.人类​​受试者研究41 保护人类受试者（如果面部页面上的项目4标记为“是”）NA 数据和安全监控计划（如果面部页面上的项目4标记为“是”，则需要 或提出III临床试验）NA 包括妇女和少数民族（如果面部页面上的项目4标记为“是”，并且是临床研究）NA 有针对性/计划的入学表（用于新的和持续的临床研究）NA 包括儿童（如果面部页面上的项目4标记为“是”）NA F.脊椎动物Na G.选择代理研究NA H.文学引用41 我，多个PI领导计划46 J.财团/合同安排46 K.资源共享NA L.支持信（例如，顾问）NA 清单。 47 检查是否 附录（fiveCollat​​edSets.nopageNumberingNecessaryforappendix。）。 附录是 包括 接受出版的出版物和手稿数量（不超过10） 其他项目（列表）： PHS 398（Rev. 04/06）第4页表格页3