Bayesian inference of the mode of speciation and gene flow using genomic data

当代物种的基因组序列包含了丰富的物种分化史和物种起源信息。通过比较不同物种的DNA序列，我们可以弄清楚这些物种是如何联系在一起的，它们是什么时候彼此分化的，以及它们是否交换过基因。然而，从基因组数据中提取这些信息需要强大的统计模型和高效的计算算法。多物种聚结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，因为它适应了遗传物质世代传递时生物繁殖的随机波动、基因突变的随机积累以及物种之间可能的杂交或渐渗。我们将扩展我们的贝叶斯推理程序BPP，以允许物种之间的连续基因流动，包括隔离与迁移，隔离与初始迁移，二次接触以及完全隔离。这些模型代表了关于物种形成模式的不同生物学假设，并可以进行比较，以进一步了解物种形成过程。该项目将开发的贝叶斯方法在提取基因组数据集的信息方面是有效的，同时适应重要的生物过程，如祖先物种的多态性，由于短基因组片段序列数据中的信息有限而导致的基因谱系树的不确定性。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来自Panthera属大型猫科动物、Heliconius蝴蝶、马达加斯加鼠狐猴和北美蜥蜴的基因组数据集。我们将推断物种分化的历史，基因流动的方向和时间，以及物种分化时间和种群规模等进化参数。

Genomic sequences from contemporary species contain rich information about the history of species divergence and the origin of species. By comparing DNA sequences from different species we can work out how the species are related, when they diverged from each other, and whether they have been exchanging genes. However, powerful statistical models and efficient computational algorithms are necessary to extract this information from genomic data. The multispecies coalescent model provides a natural framework for comparative analysis of genomic sequence data, as it accommodates the random fluctuations of biological reproduction when genetic materials are passed over generations, random accumulations of genetic mutations as well as possible hybridisation or introgression between species. We will extend our Bayesian inference program BPP to allow continuous gene flow between species, including isolation-with-migration, isolation-with-initial-migration, secondary contact, as well as complete isolation. Those models represent different biological hypotheses about the modes of speciation, and can be compared to further our understanding of the speciation process. The Bayesian methods to be developed in the project are efficient in extracting information in the genomic datasets, while accommodating important biological processes involved, such as the polymorphism in the ancestral species, uncertainties in the gene genealogical trees due to limited information in the sequence data from a short genomic segment. We will apply our newly developed methods to analyse genomic datasets from the big cats in the Panthera genus, Heliconius butterflies, Malagasy mouse lemurs, and North-American lizards, generated by our collaborators. We will infer the history of species divergences, the direction and timing of gene flow, as well as evolutionary parameters such as species divergence times and population sizes.