The genomic and phenotypic basis of a biological invasion

人类的影响改变了适应环境，改变了大量物种的进化轨迹。许多物种能够生存、坚持和适应人类的生态位，但我们对人类如何间接改变特征、基因和涉及的进化过程的了解有限。家雀是一种分布广泛、富有魅力和众所周知的人类共生鸟类。我们之前已经证明，家雀在新石器时代随着早期农业社会的迁徙而从中东的原产地扩散到欧洲。然而，由于19世纪的刻意引入，家雀已经在北美、南美和澳大利亚建立起来。在新石器时代，形态和新陈代谢的变化导致了最初向依赖人类的生态位的转变，这种较新的扩散是否促进了新地区的发展？或者它是由新的适应驱动的，比如认知或免疫反应的变化？幸运的是，家雀的介绍有很好的记录，博物馆的收藏品包含从引入时到当代的标本样本。这使得有可能量化等位基因频率和表型在时间尺度上的变化，跟踪这种共生物种最近的传播，为选择和深入了解适应机制提供证据。我们建立了一个从5个地点(墨尔本、里约热内卢、纽约、多伦多和旧金山)采集的家雀数据集，在引入后20、50和100年(每个时间段15-20个样本)。利用全基因组重新测序，这个项目将首先寻求检验这样一个假设，即现代家雀的引入是由多个独立的进化谱系建立的。该项目的第二部分将是从引进的家雀种群中识别选择的基因组签名。特别是，我们希望利用我们独特的时间序列数据来重建引入过程中的等位基因频率变化，重点关注一组涉及认知、喙形状、免疫反应和消化的候选基因。结合我们当代来自该物种原生物种范围内的400个基因组的数据集，将有可能明确测试在最近的传播中是否发生了对相同基因的选择。除了基因组数据，我们还可以访问博物馆的收藏品，其中包括在过去141年中收集的1974只家雀个体。该项目将使用3D形态测量学和摄影测量学来识别引入家雀后的表型进化，重点是头面部形态。该项目的首要目标是了解在进化背景下依赖人类的类群的传播情况，并阐明生物入侵的基因组和表型基础。

Human impact has altered the adaptive landscape and has shifted the evolutionary trajectories of a huge number of species. Many species are able to survive, persist and adapt to a human niche, yet our knowledge of how humans indirectly alter traits, genes and the evolutionary processes involved is limited. The house sparrow (P. domesticus) is a widespread, charismatic and well-known example of a human-commensal bird. We have previously shown that the house sparrow spread from its native range in the Middle East into Europe alongside the movement of early agricultural societies during the Neolithic. However, due to deliberate introductions during the 19th Century, house sparrows have established in North America, South America and Australia. Has this more recent spread to new regions been facilitated by the same morphological and metabolic changes that led to the original shift to a human-dependent niche during the Neolithic? Or has it been driven by new adaptations such as changes in cognition or immune response? Fortunately, house sparrow introductions are well-documented and museum collections contain specimens sampled from the time of introduction to contemporary periods. This makes it possible to quantify changes in allele frequencies and phenotypes across the temporal scale that tracks the recent spread of this commensal species, providing evidence of selection and insight into adaptive mechanisms.We have established a dataset of house sparrows sampled from 5 locations (Melbourne, Rio de Janeiro, New York, Toronto and San Francisco) at 20, 50 and 100-years post-introduction (15-20 samples per time period). Using whole genome resequencing, this project will first seek to test the hypothesis that modern house sparrow introductions have been founded by multiple independent evolutionary lineages. The second part of the project will be to identify genomic signatures of selection in populations from the introduced range of the house sparrow. In particular, we hope to use our unique time-series data to reconstruct allele frequency changes during the course of the introduction, focusing on a set of candidate genes involving cognition, beak shape, immune response and digestion. Combined with our contemporary dataset of >400 genomes from across the native range of the species, it will be possible to explicitly test whether selection has occurred on the same genes in the more recent spread. In addition to genomic data, we have access to museum collections with 1974 house sparrow individuals collected over the last 141 years. The project will use 3D morphometrics and photogrammetry to identify phenotypic evolution in house sparrows following introduction, focusing on craniofacial morphology. The overarching aim of this project is to understand the spread of anthrodependent taxa in an evolutionary context and to shed light on the genomic and phenotypic basis of a biological invasion.