Bayesian implementation of the multispecies-coalescent-with-introgression (MSci) model for analysis of population genomic data

用于群体基因组数据分析的多物种合并渗入 (MSci) 模型的贝叶斯实施

• 批准号: BB/T003502/1
• 负责人: Ziheng Yang
• 金额: $ 55.91万
• 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: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FT003502%2F1
• 关键词: Bayesian; implementation; multispecies; coalescent; introgression

Genomes from different species contain rich information about the evolutionary history of the species. By comparing DNA sequences from different species or different individuals of the same species we can work out how the species are related, when they diverged from each other, whether and when there was cross-species hybridisation. Nevertheless, to extract this information from our genomes, powerful statistical models and efficient computational algorithms are necessary. The multispecies-coalescent-with-introgression (MSci) model provides a natural framework for comparative analysis of genomic sequence data, accommodating the random fluctuations of biological reproduction when genetic materials are passed over generations, random accumulations of genetic mutations as well as possible cross-species hybridisation events. We will implement the MSci model in our Bayesian Markov chain Monte Carlo simulation program, so that it can be used to estimate species phylogenies and species divergence times, ancestral population sizes, and the time and rate of hybridisation. Those parameters will provide important insights into the origin of species. We will apply our newly developed methods to analyse genomic datasets from Heliconius butterflies, Malagasy mouse lemurs, and lizards, generated by our collaborators.

来自不同物种的基因组包含有关该物种进化历史的丰富信息。通过比较不同物种或同一物种不同个体的 DNA 序列，我们可以弄清楚物种之间的关系、它们何时彼此分化、是否以及何时存在跨物种杂交。然而，为了从我们的基因组中提取这些信息，强大的统计模型和高效的计算算法是必要的。多物种合并与渐渗（MSci）模型为基因组序列数据的比较分析提供了一个自然的框架，适应遗传物质代代相传时生物繁殖的随机波动、基因突变的随机积累以及可能的交叉。物种杂交事件。我们将在我们的贝叶斯马尔可夫链蒙特卡罗模拟程序中实施 MSci 模型，以便它可以用于估计物种系统发育和物种分化时间、祖先种群规模以及杂交的时间和速率。这些参数将为物种起源提供重要的见解。我们将应用我们新开发的方法来分析由我们的合作者生成的 Heliconius 蝴蝶、马达加斯加鼠狐猴和蜥蜴的基因组数据集。

项目成果

Efficient Bayesian inference under the multispecies coalescent with migration.

多物种与迁移结合下的有效贝叶斯推理。

• DOI: http://dx.10.1073/pnas.2310708120
• 发表时间: 2023
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Flouri T

Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks.

贝叶斯和启发式测试的力量，参考北美花栗鼠 Tamiasquadrivittatus 群体的基因流来检测跨物种渗入。

• DOI: http://dx.10.1093/sysbio/syac077
• 发表时间: 2023
• 期刊: Systematic biology
• 影响因子: 6.5
• 作者: Ji J

Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.

基因组规模数据揭示了美国西南部和中部德克萨斯角蜥蜴（Phrynosoma cornutum）的深刻谱系分歧和复杂的人口统计历史。

• DOI: http://dx.10.1093/gbe/evab260
• 发表时间: 2022
• 期刊: Genome biology and evolution
• 作者: Finger N

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

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