The genomic and phenotypic basis of a biological invasion

人类的影响已经改变了适应性景观，并改变了大量物种的进化轨迹。许多物种能够生存、坚持并适应人类的生态位，但我们对人类如何间接改变特征、基因和进化过程的了解有限。家雀（P. domesticus）是一种广泛存在的、有魅力的、众所周知的人类共栖鸟类。我们之前已经证明，家雀随着新石器时代早期农业社会的运动，从中东的原生范围传播到欧洲。然而，由于19世纪有意引入，家麻雀已经在北美、南美和澳大利亚建立起来。这种最近向新地区的传播是否受到了新石器时代导致最初转向依赖人类的生态位的相同形态和代谢变化的促进？或者它是由认知或免疫反应的变化等新的适应所驱动的？幸运的是，家雀的引进有很好的记录，博物馆收藏了从家雀引进到当代的标本。这使得在时间尺度上量化等位基因频率和表型的变化成为可能，从而跟踪这种共生物种最近的传播，为选择和适应机制提供证据。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）在引入后20、50和100年（每个时间段15-20个样本）取样的家雀数据集。利用全基因组重测序，该项目将首先试图验证现代家雀的引入是由多个独立的进化谱系建立的假设。该项目的第二部分将是确定家雀引进范围内种群选择的基因组特征。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，免疫反应和消化的候选基因。结合我们现有的来自该物种原生范围的400个基因组数据集，将有可能明确测试在最近的传播中是否发生了相同基因的选择。除了基因组数据，我们还可以访问过去141年里收集的1974只麻雀的博物馆藏品。该项目将使用3D形态测量学和摄影测量学来识别家雀的表型进化，重点关注颅面形态。该项目的总体目标是了解人类依赖类群在进化背景下的传播，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.