Detecting genomic signatures of ecological speciation and parallel evolution in oaks

尽管达尔文的中心思想——自然选择驱动物种形成——被广泛接受，但它可能导致生殖隔离的机制，以及面对持续的基因流动，物种完整性的起源和维持在很大程度上仍然未知。该项目解决了进化生物学中的这个核心问题，提供了额外的证据，证明朝着不同最优的不同选择可以在面对基因流动时保持物种的完整性，并可能导致新物种的进化（生态物种形成）。同域、多物种栎群落是研究基因组水平上基因流动的生态物种形成过程的模型系统。因此，杂交在栎树中很常见，而欧洲白栎树（Quercus section Quercus）和北美红栎树（Quercus section Lobatae）的物种边界是出了名的弱。然而，这些物种之间反复的基因流动并没有导致遗传凝聚力或适应性独特性的丧失，有证据表明，生态驱动的选择在限制有效的种间基因流动方面起着重要作用。基于基因的微卫星标记筛选和基因组扫描揭示了具有强分化选择的基因，这些基因可能对物种间的适应性分化和生殖隔离产生潜在影响。本项目将重点研究白栎树群的两个杂交姊妹种，栎木（Quercus robur）和栎木（Quercus pepeea），以及红栎树群的栎木（Q. ellipsoidalis）和栎木（Q. rubra），它们对干旱有不同的适应能力。该项目将使用全基因组重测序技术生成多个种群对的全基因组数据(1)，以表征不同选择的全基因组模式；(2)识别物种间适应性差异和生殖隔离的候选基因，即生命之树的形状谱系差异。鉴定参与物种形成和物种完整性维持的基因的研究很少，但在我们的栎树模型系统中持续的基因流动，加上不同的选择，允许鉴定选择下的基因（异常位点）和抵抗种间基因流动均质化力的相关基因组区域。整合目前在Q. robur和Q. rubra中构建的高密度遗传连锁图谱的全基因组异常点筛选，我们将表征异常位点的全基因组分布。为此，我们将在已测序和注释的黑桫树基因组的框架上定位黑桫树和黑桫树的连锁图谱，以确定异常基因和与物种间生殖隔离有关的候选基因的基因组位置。该项目为鉴定橡树中涉及适应性分化和生殖隔离的基因以及理解橡树生命之树的适应性分化奠定了基础。

Even though Darwin’s central idea that natural selection drives speciation is widely accepted, the mechanisms by which it may lead to reproductive isolation and the origin and maintenance of species integrity in the face of ongoing gene flow are still largely unknown. This project addresses this central question in evolutionary biology to provide additional evidence that divergent selection towards different optima can maintain species integrity in the face of gene flow and could have resulted in the evolution of new species (ecological speciation). Sympatric, multispecies oak (Fagaceae: Quercus) communities are model systems to study processes of ecological speciation with gene flow at the genome level. Thus, hybridization is common among oaks, and species boundaries in European white oaks (Quercus section Quercus) and in the North American red oaks (Quercus section Lobatae) are notoriously weak. However, recurrent gene flow among these species has not led to a loss of genetic cohesiveness or adaptive distinctness, and there is evidence that ecologically-driven selection plays an important role in limiting effective interspecific gene flow. Screening of gene-based microsatellite markers and genome scans revealed genes under strong divergent selection with potential effect on both adaptive divergence and reproductive isolation between species. This project will focus on the two hybridizing sister species of the white oak group, Quercus robur and Quercus petraea, and of the red oak group, Q. ellipsoidalis and Q. rubra, that have distinct and varied adaptations to drought. The project will be generating genome-wide data data across multiple population pairs using Whole Genome Resequencing (1) to characterize genome-wide patterns of divergent selection and (2) to identify candidate genes for adaptive divergence and reproductive isolation between species the shaped lineage divergence across the oak tree of life. Studies identifying genes involved in speciation and maintenance of species integrity are rare, but ongoing gene flow in our Quercus model system, coupled with divergent selection, allows for the identification of genes under selection (outlier loci) and of linked genomic regions that resist the homogenizing force of interspecific gene flow. Integrating genome-wide outlier screens with high density genetic linkage maps that are currently constructed in Q. robur and in Q. rubra we will characterize the genome-wide distribution of outlier loci. For this purpose, both Q. robur and Q. rubra linkage maps will be anchored to scaffolds of the sequenced and annotated Q. robur genome to identify the genomic location of outlier genes and of physically linked candidate genes with putative role in reproductive isolation between species. The proposed project forms the foundation for the identification of genes involved in adaptive divergence and reproductive isolation in oaks and for understanding adaptive divergence across the oak tree of life.