Phylogeographic inference using genomic sequence data under the multispecies coalescent model

多物种合并模型下使用基因组序列数据进行系统发育地理学推断

• 批准号: BB/P006493/1
• 负责人: Ziheng Yang
• 金额: $ 50.8万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP006493%2F1
• 关键词: Phylogeographic; inference; using; genomic; sequence

Our evolutionary history is written in our genomes. By comparing DNA sequences from different species or multiple individuals of the same species we can work out how the species are related, when they diverged from each other, whether there was introgression between the species, and whether the population size of a species went through a bottleneck or other demographic changes. DNA sequences can also be used to identify species and delineate species boundaries. To address such exciting questions, powerful statistical methods and computational algorithms are necessary. In this project we will develop new statistical models and computer algorithms for efficient analysis of genomic sequence data within two well-established statistical frameworks: maximum likelihood and Bayesian inference. We will develop a maximum likelihood method for estimating the species tree that accommodates the random process of biological reproduction and genetic sequence evolution, as well as introgression or hybridisation that may be common between closely related species, especially during radiative speciations. We will introduce significant improvements and extensions to our Bayesian model-comparison approach to delimiting species using genomic sequence data. We will implement sophisticated models to describe the evolutionary process of DNA sequences and to allow changes in the evolutionary rate among lineages so that the program can be applied to estimate species phylogenies for distantly related species, such as different orders of mammals. We will parallelize the program to improve the computational efficiency.

我们的进化史写在我们的基因组中。通过比较不同物种或同一物种多个个体的DNA序列，我们可以了解物种之间的关系、何时彼此分化、物种之间是否存在基因渗入以及物种的种群规模是否经历了基因渗入。瓶颈或其他人口变化。 DNA 序列还可用于识别物种并划定物种边界。为了解决这些令人兴奋的问题，强大的统计方法和计算算法是必要的。在这个项目中，我们将开发新的统计模型和计算机算法，以便在两个完善的统计框架内有效分析基因组序列数据：最大似然和贝叶斯推理。我们将开发一种最大似然方法来估计物种树，该方法适应生物繁殖和基因序列进化的随机过程，以及密切相关物种之间可能常见的基因渗入或杂交，特别是在辐射物种形成过程中。我们将对贝叶斯模型比较方法进行重大改进和扩展，以使用基因组序列数据来界定物种。我们将实现复杂的模型来描述 DNA 序列的进化过程，并允许谱系之间进化速率的变化，以便该程序可以应用于估计远缘物种的物种系统发育，例如哺乳动物的不同目。我们将对程序进行并行化以提高计算效率。

项目成果

The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics.

分子系统发育中 Bootstrap 支持值的渐近行为。

• DOI: http://dx.10.1093/sysbio/syaa100
• 发表时间: 2021
• 期刊: Systematic biology
• 影响因子: 6.5
• 作者: Huang J

Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.

多物种合并及其在推断物种系统发育和跨物种基因流中的应用。

• DOI: http://dx.10.1093/nsr/nwab127
• 发表时间: 2021
• 期刊: National science review
• 影响因子: 20.6
• 作者: Jiao X

A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model.

检验多物种合并模型下系统发育组数据集中信息内容的模拟研究。

• DOI: http://dx.10.1093/molbev/msaa166
• 发表时间: 2020
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Huang J

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

使用基因组序列和多物种合并的 BPP 进行物种树推断

• DOI: 10.1093/molbev/msy147
• 发表时间: 2018-10-01
• 期刊: Molecular Biology and Evolution
• 影响因子: 10.7
• 作者: Flouri T;Jiao X;Rannala B;Yang Z
• 通讯作者: Yang Z

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model.

二倍体基因组中杂合位点的相位解析对于多物种合并模型下的系统发育分析很重要。

• DOI: http://dx.10.1093/sysbio/syab047
• 发表时间: 2022
• 期刊: Systematic biology
• 影响因子: 6.5
• 作者: Huang J