Gene Tree-Species Tree Relationships Under the Coalescent Process

[摘要]项目ID: DMS-0505265 Prev项目编号：0104290 PI: Salter， Laura机构：New Mexico大学标题：基因树-物种树关系在聚幼变过程中。在本论文中，我们使用来自多个基因的数据来研究基因树和物种树的不一致性。首先，研究者将展示一种目前提倡的多基因数据分析方法，即串联方法，即使使用一致的系统发育树估计方法，也可能在统计上不一致。其次，在聚结模型下，将开发并实现从多个基因数据中对物种树进行最大似然估计的算法，并将通过互联网免费提供。ML物种树估计方法的可用性将允许基于似然的假设检验系统地理学和群体遗传假设。此外，评估物种树估计不确定性的方法将通过扩展系统遗传学中传统的自举方法来开发，以便在整个基因组中随机采样多个基因的情况下收集数据。最后，将通过检查观察到的基因树是否与给定的物种树一致，使用几个指标来测量不一致的水平，从而开发出聚结模型的充分性测试。基于包含在生物体DNA序列中的信息来推断生物体的进化史是进化生物学中一个至关重要的问题。基因组测序项目产生的大量DNA序列数据导致了这些系统发育关系推断的重大挑战。这些挑战之一是基于基因组中几个不同基因的DNA序列信息来推断物种集合的进化史。本项目利用多基因数据研究聚结过程对物种系统发育推断的影响。这项工作将首先证明，未能建立凝聚过程的模型可能导致物种关系的错误推断。然后，研究者将开发方法，通过明确建模成结过程来准确估计物种系统发育，并将这些估计程序应用于构建假设检验和测量估计物种系统发育不确定性的技术

Abstract Prop ID: DMS-0505265 Prev Awd: 0104290 PI: Salter, Laura Institution: University of New Mexico Title: Gene Tree-Species Tree Relationships Under the Coalescent Process In this proposal, incongruence in gene trees and species trees isexamined using data from multiple genes in the context of thecoalescent process. First, the investigator will showthat one currently advocated approach for the analysis of datafrom multiple genes, the concatenation approach, can bestatistically inconsistent, even when a consistent method ofphylogenetic tree estimation is used. Second, an algorithm formaximum likelihood (ML) estimation of species trees from data onmultiple genes under the coalescent model will be developed andimplemented, and will be made freely available via the internet.The availability of a method for ML species tree estimation willallow for likelihood-based hypothesis testing of phylogeographicand population genetic hypotheses. Further, methods for assessinguncertainty in the species tree estimates will be developed byextending traditional bootstrapping methods in phylogenetics tothe case in which data have been collected for multiple genessampled randomly throughout the genome. Finally, tests for theadequacy of the coalescent model will be developed by examiningwhether the observed gene trees are consistent with a givenspecies tree using several metrics to measure levels ofincongruence.The inference of the evolutionary history of a collection of organisms based on the information contained in their DNA sequences is a problemof fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant challenges in the inference of these phylogenetic relationships. Among these challenges is the inference of the evolutionary history of a collection of species based on DNA sequence informationfrom several distinct genes sampled throughout the genome. This project studies the effect of the coalescent process on the inference of species phylogenies using data from multiple genes. This work will first demonstrate that failure to model the coalescent process can lead to incorrect inferences of species relationships. The investigator will then develop methods that can accurately estimate species phylogenies through explicitly modeling the coalescent process, and will apply these estimation procedures to construct techniques for hypothesis testing and for measuring uncertainty in estimated species phylogenies.--