Gene Tree-Species Tree Relationships Under the Coalescent Process

摘要项目ID：DMS-0505265上一页Awd：0104290 PI：Salter，Laura 研究机构：新墨西哥州大学题目：基因树-物种树在合并过程中的关系 在这个建议中，不一致的基因树和物种树是检查使用的数据，从多个基因的背景下，thecoalescent过程。 首先，研究者将表明，一个目前提倡的方法，从多个基因的数据分析，连接的方法，可以是统计上不一致的，即使是一个一致的方法ofphylogenetic tree估计使用。其次，将开发和实现一种算法，用于在联合模型下从多个基因的数据对物种树进行最大似然（ML）估计，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地理和种群遗传假设。 此外，评估物种树估计的不确定性的方法将通过扩展遗传学中的传统自举方法来开发，以用于在整个基因组中随机采样的多个基因的数据已经收集的情况。 最后，将通过检验所观察到的基因树是否与一个给定的物种树一致来检验结合模型的充分性。使用几个度量标准来衡量不一致的程度。根据生物体DNA序列中所包含的信息来推断一个生物体集合的进化历史是进化生物学中一个至关重要的问题。从基因组测序项目产生的DNA序列数据的丰富性，导致了这些系统发育关系的推断的重大挑战。这些挑战之一是根据DNA序列信息推断一系列物种的进化历史，这些信息来自整个基因组中取样的几个不同基因。 本计画利用多基因资料，研究结合过程对物种遗传推论的影响。 这项工作将首先证明，未能模拟聚结过程可能会导致物种关系的不正确推断。 然后，研究人员将开发出可以通过明确建模的聚结过程准确估计物种遗传的方法，并将这些估计程序应用于构建假设检验和测量估计物种遗传不确定性的技术。

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.--