Data: Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere

Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced ranges of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele-sharing and demographic modelling we show that Z. indinaus have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of Z. indianus’s introduced range; or, more parsimoniously, that Z. indianus has experienced selection early on during (or prior-to) its expansion into the western hemisphere. We suggest that the range expansion of Z. indianus has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere.

Methods
Data tables summarise results produced as part of a study of genetic differentiation among populations of the African fig fly, Zaprionus indianus. Please see ReadMe file for details of what is contained within each file.

外来物种已成为全球各地生物群落中愈发常见的组成部分。因此，入侵生物学（invasion biology）的核心目标之一，便是阐明支撑成功引种的种群统计与演化因素。本研究针对非洲无花果果蝇（African fig fly, Zaprionus indianus）的原生分布区与引种分布区种群采集全基因组序列（whole genome sequences），以此量化种群间的遗传亲缘关系，确定引种事件的潜在源头种群，并在不同空间尺度下开展选择作用检测。我们发现，西半球地理分布广泛的种群彼此间的遗传相似性高于其与非洲各采样支系的遗传相似性，且这些种群携带来自分化程度各异的非洲支系的混合等位基因。通过等位基因共享模式与种群统计建模分析，我们证实印度无花果果蝇（Zaprionus indianus）曾经历一次横跨西半球的种群扩张，且该扩张发生前，不同非洲支系间已存在基因混合事件。我们还发现了西半球种群间存在共有的选择信号的证据，在部分案例中，这类选择信号还与部分非洲种群共享。这表明存在两种可能性：其一，平行选择在印度无花果果蝇引种分布区的广大区域内发挥作用；其二，更符合简约性原则的解释是，印度无花果果蝇在向西半球扩张的过程中（或扩张之前）的早期阶段便已经历选择作用。我们提出，印度无花果果蝇的分布区扩张得益于基因混合与选择作用，针对该入侵物种的防控工作可聚焦于通过管控该区域内的个体移动（而非跨东西半球的个体流动），以减少后续的基因混合事件。
方法
本数据集的数据表汇总了针对非洲无花果果蝇（African fig fly, Zaprionus indianus）种群遗传分化的研究结果。各文件的具体内容请参阅ReadMe文件。