Adaptive introgression in the Anthropocene

人类对物种的迁移和人为气候变化导致了一些前所未有的物种分布变化速度，导致许多本地和非本地物种聚集在一起。虽然生态后果经常被充分记录，但本地和非本地物种之间杂交和基因流动的进化影响通常不太明显。然而，本地和非本地物种之间的基因流动可能会深刻影响未来的进化适应和多样化，潜在地影响物种保护、对气候变化的反应和入侵物种的传播。以前的研究只关注几个典型物种之间的基因流动。因此，我们对跨生命之树的种间基因流动的普遍性和影响缺乏一般的了解，特别是人类活动如何改变这些基因流动的速度。在这个雄心勃勃的提议中，我们将利用达尔文生命之树项目产生的参考基因组，并将高通量测序与最新的生物信息学方法相结合，以解决一个日益重要的主要问题：本地和非本地开花植物物种之间的基因流动程度如何，这种基因流动对本地或非本地物种具有适应价值吗？我们将首次使用已知在不列颠群岛杂交的106种本地/非本地开花植物物种对来评估生命之树主要分支的基因流动。然后，我们将使用这些数据来参数化模型，预测本地和非本地物种之间的基因流动速率，并测试模型估计未观察到杂交的物种对之间的隐基因流动。英国植物群被深入研究，其良好的特征分布，杂交和生态使其成为一个理想的模型系统，用于建立预测模型，探索影响本地和非本地物种之间基因流动速率和效果的生态和遗传因素。在这个项目的过程中，我们将产生24万亿个碱基的序列数据，包括来自269种开花植物的741个个体的基因组（137种原生植物，132种非原生植物）。我们将利用这些数据首先评估所有106种已知在不列颠群岛杂交的本地/非本地开花植物物种对之间的基因流动程度（目标1），并确定其中一些物种最近的范围扩大是否与基因流动增加有关（目标2）。然后，种群样本将用于评估目标1和2中显示适应性渗入迹象的10个受体物种子集中适应性基因流动的证据（目标3）。我们将使用目标1和目标2的渗入估计来建立统计模型，以了解影响基因流动的遗传和生态因素（目标4）。最后，我们将使用额外的菊科（菊花科）和禾草科（禾草）17个属的基因流的经验估计来测试评估模型预测未杂交物种之间隐基因流的准确性（目标5）。这个项目将是理解人类介导的物种间基因流动的进化后果的重要一步。种间杂交很可能广泛存在，但由于受精卵后的生殖障碍，基因流动仍可能受到限制。另外，物种之间的基因流动可能是普遍的，并且具有很强的适应性。除了学术上的受益者（进化和全球变化生物学家），我们的结果将为保护从业者提供信息，控制入侵物种，并提高公众对物种间基因流动的普遍性和重要性的认识，以及对环境变化的进化反应。

Human translocation of species and anthropogenic climate change are resulting in some of the fastest rates of species distribution changes ever seen, causing many native and non-native species to be brought together. While the ecological consequences are often well-documented, the evolutionary impacts of hybridization and gene flow between native and non-native species are usually less visible. Yet gene flow between native and non-native species could profoundly affect future evolutionary adaptations and diversification, potentially impacting on species conservation, responses to climate change and the spread of invasive species. Previous studies have only focussed on gene flow between a few exemplar species. So we lack a general understanding of the prevalence and impact of interspecific gene flow across the tree of life, and specifically of how human activities may be altering these rates of gene flow.In this ambitious proposal, we will leverage reference genomes produced by the Darwin Tree of Life project and combine high-throughput sequencing with the latest bioinformatic methods to address a major question of growing importance: What is the extent of gene flow between native and non-native flowering plant species, and is this gene flow of adaptive value to native or non-native species? We will for the first time assess gene flow across a major branch of the tree of life using all 106 native/non-native flowering plant species pairs known to be hybridising in the British Isles. We will then use these data to parameterise models predicting the rate of gene flow between native and non-native species, and test model estimates of cryptic gene flow among species pairs that have not been observed to hybridize. The British flora is intensively studied, and its well characterised distributions, hybrids and ecology make it an ideal model system to build predictive models exploring ecological and genetics factors affecting the rates and effects of gene flow between native and non-native species.Over the course of this project we will generate 24 trillion bases of sequence data, comprising the genomes of 741 individuals from 269 flowering plant species (137 native, 132 non-native). We will use this data to first assess the extent of gene flow between all 106 native/non-native flowering plant species pairs that are known to hybridise in the British Isles (Objective 1), and establish whether the recent range expansions seen in some of these species are associated with increased gene flow (Objective 2). Population samples will then be used to assess evidence for adaptive gene flow in a subset of 10 recipient species that from Objective 1 and 2 show indications of adaptive introgression (Objective 3). We will use the estimates of introgression from Objectives 1 and 2 to build statistical models to understand the genetic and ecological factors affecting gene flow (Objective 4). Finally, we will test assess the accuracy of model predictions of cryptic gene flow between species that are not known to hybridize using additional empirical estimates of gene flow from 17 genera of Asteraceae (daisy family) and Poaceae (grasses) (Objective 5). This project will be a major step towards understanding the evolutionary consequences of human-mediated gene flow between species. Interspecific hybridization could well be widespread, yet gene flow may still be restricted because of postzygotic reproductive barriers. Alternatively, gene flow between species may be common, and with strong fitness consequences. In addition to academic beneficiaries (evolutionary and global change biologists), our results will inform conservation practitioners, control of invasive species, and increase awareness in the general public about the ubiquity and importance of gene flow among species, and evolutionary responses to environmental change.