Abstract
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.
Highlights
Human modification of the environment has greatly accelerated the rate of global biodiversity loss in recent decades [1,2]
We demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for Genotyping-in-Thousands by sequencing (GT-seq) panel development for informing biodiversity conservation in other systems
It is important to highlight, that GT-seq panel development was greatly facilitated by the existence of an archipelago-wide single nucleotide polymorphisms (SNPs) dataset previously collected via double-digest restriction-site associated DNA (ddRAD) [25]
Summary
Human modification of the environment has greatly accelerated the rate of global biodiversity loss in recent decades [1,2]. A leading driver of these losses is the introduction of non-native species to new environments. Once established, these invasive alien species (IAS) can alter ecosystem dynamics, especially through predation, competition, and disease transmission, resulting in rapid declines to endemic species [3,4]. The United States spends >US$220 billion annually in prevention efforts, damages, and habitat restoration [8]. These negative effects are amplified within island systems, evidenced by IAS being the leading cause of the majority (86%) of recent island extinctions [3]. Insular systems support disproportionately high levels of endemism relative to mainland areas [9], punctuating the need for immediate action towards improving IAS management on islands
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