Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

<b>Abstract</b><br/><p>Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n=295) and black rats (n=241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.</p>

<b>摘要</b><br/><p>外来入侵物种（Invasive alien species, IAS）是全球生物多样性丧失的主要原因之一。其中，入侵性褐家鼠（Rattus norvegicus）和黑家鼠（R. rattus）是岛屿物种灭绝的主导驱动因素，尤其对于海鸟而言——超过50%的海鸟灭绝事件可归因于鼠类捕食。根除是入侵鼠类管理的核心策略，但该策略在全球岛屿上的失败率约为10%-38%。遗传工具（Genetic tools）可助力IAS管理决策，然而迄今为止这类应用多为被动响应式，耗时且成本高昂。在此，我们开发了一种基于测序的数千基因分型（Genotyping-in-Thousands by sequencing, GT-seq）面板（命名为RapidRat），用于加拿大不列颠哥伦比亚省中部海岸外由约150个岛屿组成的海达瓜伊（Haida Gwaii）群岛中入侵性褐家鼠与黑家鼠的快速物种鉴定及种群溯源。我们利用海达瓜伊群岛全域采集的褐家鼠（n=295）和黑家鼠（n=241）的双酶切限制性位点关联DNA（double-digest restriction-site associated DNA, ddRAD）基因型数据（27686个单核苷酸多态性位点），构建了包含443个单核苷酸多态性位点（single nucleotide polymorphism, SNP）的优化面板。通过与ddRAD结果对比，我们验证了该面板在个体物种鉴定及原产地岛屿溯源方面的信息有效性；所有对比显示，利用RapidRat估算的混合系数（admixture coefficient）与种群溯源结果均保持一致。为展示应用价值，我们对三个岛屿（Agglomerate岛、Hotspring岛、Ramsay岛）新入侵事件中的20个个体进行RapidRat基因分型，所有样本均被高置信度（概率>98.5%）溯源至Faraday岛和Murchison岛作为潜在来源种群（putative source population）。这些结果表明，此前在Hotspring岛实施的根除行动地理尺度不当；未来管理应扩大根除单元，将邻近岛屿纳入以防止再次入侵。综上，我们证明RapidRat是海达瓜伊群岛入侵鼠类种群管理的有效工具，并为GT-seq面板开发提供了清晰框架，以助力其他生态系统的生物多样性保护决策。</p>