Gene Tree-Species Tree Relationships Under the Coalescent Process

摘要Prop ID：dms-0505265 Prev AWD：0104290 PI：Salter，Laura Institution：New墨西哥大学标题：基因树-物种树在合并过程下的关系在本提案中，基因树和物种树的不一致性是使用来自多个基因的数据在更年期过程的背景下进行检验的。首先，研究人员将证明，目前提倡的一种分析多基因数据的方法，即串联方法，即使使用一致的系统发育树估计方法，在统计上也可能是不一致的。其次，将开发和实现一个在联合模型下从多个基因的数据中估计物种树的最大似然(ML)算法，并将通过互联网免费提供该算法。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和种群遗传假设。此外，通过将系统发育学中的传统自举方法扩展到已经收集了在整个基因组中随机抽样的多个基因的数据的情况，将开发评估物种树估计的不确定性的方法。最后，结合模型的充分性测试将通过使用几个度量标准来检验观察到的基因树是否与给定物种树一致来进行。基于包含在其DNA序列中的信息来推断一组生物的进化历史是进化生物学中的一个基本问题。基因组测序项目产生的丰富的DNA序列数据导致了对这些系统发育关系推断的重大挑战。这些挑战之一是根据DNA序列信息推断一组物种的进化史，这些DNA序列信息来自于整个基因组中采样的几个不同的基因。这个项目使用来自多个基因的数据来研究合并过程对物种系统发育推断的影响。这项工作将首先证明，未能对合并过程进行建模可能会导致对物种关系的错误推断。然后，研究人员将开发可以通过明确地模拟合并过程来准确估计物种系统发育的方法，并将应用这些估计程序来构建用于假设检验和测量估计的物种系统发育的不确定性的技术。

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.--