Genome-wide analysis of speciation and adaptation in closely related plant species

这个项目致力于生物学中最持久的问题之一/物种是如何形成的。我们对物种形成过程理解的最新进展，即物种形成的基因观表明，不同的基因可能具有不同的能力，跨越物种边界，进入密切相关的物种。正向选择下的基因有望在许多密切相关的物种中传播，即使这些物种的杂交非常罕见。几个密切相关物种的这种适应等位基因的“共享”可能会显著加快适应过程。另一方面，多样性选择下的基因(即不同的等位基因在不同物种中是有利的)预计不会进入，并可能导致所谓的‘基因组物种形成岛’/基因组区域的形成，这些基因岛/区域与多样性选择下的基因紧密相连，不会在物种之间入侵。因此，在基因物种形成模型下，物种边界被认为是半渗透的或“多孔的”。然而，这种物种形成观点的普遍性并不清楚，因为我们不知道物种边界有多“漏洞百出”。利用最新的基因组测序技术，我们将研究两个密切相关的植物--宽叶石杉和石竹科植物--大叶石杉和石竹科植物之间差异的遗传基础。这些种在欧洲广泛分布；它们的分布范围广泛重叠，并且已知它们经常在接触的地区形成杂交。然而，尽管这两个物种交换了基因，但它们仍然截然不同。该项目将特别关注在宽叶植物和野生植物之间正在进行的基因流动中物种边界的维护。我们将使用高通量基因组测序仪来确定从野生种群中采样的每个物种的15个个体的蛋白质编码序列。这个数据集将包括基因组中相当大比例的基因，这将使我们能够分析在两个物种之间有多大比例的基因正在经历导入，以及多大比例的基因保持分离。我们还将在任何一个物种或两个物种中确定正选择下的基因，并测试这些基因是否更容易在物种之间进行种间互渗。该数据集还将用于研究物种之间的全基因组表达差异。对蛋白质编码区DNA多态和分歧的全基因组分析将使我们能够测试现代适应和物种形成理论。

This project is devoted to one of the most enduring questions in biology / how do species form. The most recent development in our understanding of the speciation process, the genic view of speciation, suggests that different genes may have different capacities to cross the species boundaries and introgress into closely related species. The genes under positive selection are expected to spread across many closely related species even if hybridization of such species is very rare. Such 'sharing' of adaptive alleles by several closely related species may significantly accelerate the adaptation process. On the other hand, genes under diversifying selection (i.e. different alleles are advantageous in different species) are not expected to introgress and may result in formation of so called 'genomic speciation islands' / regions of the genome that are closely linked to genes under diversifying selection and that do not introgress between species. Thus, under the genic speciation model the species boundaries are regarded as semi-permeable or 'porous'. However, the generality of such a view of speciation is not clear, as we do not know how 'porous' the species boundaries are. Using the latest genomic sequencing technology we will study the genetic basis of differences between two closely related plant species, Silene latifolia and S. dioica (Caryophillaceae). These species are widely distributed in Europe; their ranges broadly overlap and they are known to often form hybrids in areas of contact. However, the two species remain distinct despite the fact that they exchange genes. This project will specifically focus on the maintenance of species boundaries in face of on-going gene flow between S. latifolia and S. dioica. We will use a high-throughput genomic sequencer to determine the protein-encoding sequence in 15 individuals of each species sampled from wild populations. This dataset will include a significant proportion of genes in the genome, which will allow us to analyse what proportion of genes is undergoing introgression and what proportion stays separate between the two species. We will also identify genes under positive selection in either or both species and will test whether these genes are more or less prone to interspecific introgression between the species. The dataset will also be used to study genome-wide expression differences between the species. The genome-wide analysis of DNA polymorphism and divergence in the protein-coding regions will allow us to test modern theories of adaptation and speciation.