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

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.