Invasive species are one of the greatest threats to biodiversity, with endemic species on islands being at particular risk. Management programs can help to minimize these impacts, but such programs are most successful when they are well-informed. In the Galápagos Islands, Ecuador, a recently introduced avian parasitic fly, Philornis downsi, has had strong negative effects on the survival of multiple endemic bird species, including several species of Darwin’s finches. The fly now populates most of the major islands within the Archipelago and the need to better understand the population structure and connectivity patterns of this invasive fly has become increasingly apparent as various management efforts are being considered. Here, we use genomic and phylogenetic approaches to estimate population structure and connectivity for P. downsi collected from five islands within the Galápagos Islands and several sites in mainland Ecuador, which is the presumptive origin of the invasive population. Genomic data showed very little genetic differentiation between island populations of P. downsi relative to the mainland. Phylogenetic analyses, which used more conservative genetic markers than the genomics approach, showed that island and mainland populations of flies were highly related. Our study provides some of the first results using genetic data to quantify differentiation among mainland and island populations of P. downsi. In addition, our study found very little genetic differentiation between island populations of flies, suggesting that there may be considerable gene flow among islands; however, further sampling is needed to determine the extent to which this could be occurring. As management techniques aimed at controlling the impact of this parasite on endemic bird populations are being considered, our study provides important insights into the history of P. downsi’s invasion to the Galápagos Islands and current population connectivity patterns.

入侵物种是对生物多样性的最大威胁之一，岛上的特有物种尤其容易受到威胁。管理程序可以帮助最大程度地减少这些影响，但是，在了解情况时，此类程序最成功。在厄瓜多尔的加拉帕戈斯群岛上，最近引进了一种鸟类寄生蝇Philornis downsi，对多种地方性鸟类，包括达尔文雀类的几种物种的生存产生了强烈的负面影响。现在，苍蝇遍布群岛内的大多数主要岛屿，并且由于正在考虑各种管理工作，因此越来越需要了解这种侵入性苍蝇的种群结构和连通性模式。在这里，我们使用基因组学和系统发育方法来估计从加拉帕戈斯群岛内的五个岛屿和厄瓜多尔大陆的多个地点收集的唐氏疟原虫的种群结构和连通性，这是入侵种群的推测来源。基因组数据显示，唐氏疟原虫岛群之间的遗传分化非常少相对于大陆。系统发育分析比基因组学方法使用了更多的保守遗传标记，表明岛上和内地苍蝇种群高度相关。我们的研究提供了一些利用遗传数据量化内陆和海岛小疫病种群分化的初步结果。另外，我们的研究发现岛上果蝇种群之间的遗传分化非常少，这表明岛上可能存在相当多的基因流动。但是，需要进一步采样以确定这种情况可能发生的程度。考虑到旨在控制这种寄生虫对特有鸟类种群影响的管理技术时，我们的研究为深入了解唐氏疟原虫的历史提供了重要见解。入侵加拉帕戈斯群岛和当前的人口连通模式。