Development of a SNP panel for geographic assignment and population
monitoring of jaguars (Panthera onca)
Abstract
The jaguar (Panthera onca) is an iconic top predator that is threatened
by habitat loss and fragmentation, along with an emerging expansion of
poaching for the illegal trade of live individuals and their parts. To
address the need for tools that improve surveillance and monitoring of
its remaining populations, we have developed a genome-enabled single
nucleotide polymorphism (SNP) panel targeting this species. From a
dataset of 58 complete jaguar genomes, we identified and selected highly
informative SNPs for geographic traceability, individual identification,
kinship, and sexing. Our panel, named ‘Jag-SNP’, comprises 459 SNPs
selected from an initial pool of 13,373,949 markers based on the
inter-biome FST, followed by rigorous filtering and addition of eight
sex-linked SNPs. We then randomly selected subsets of this panel and
identified an 84-SNP set that exhibited a similar resolving power. With
both the 459-SNP panel and its 84-SNP subset, samples were assigned with
98% success to their biomes of origin and 65-69% of them were assigned
to within 500 km of their origin. Furthermore, ca. 10-18 SNPs within
these panels were sufficient to distinguish individuals, while 6
sex-linked SNPs perfectly separated males and females. We used
whole-genome data from an additional 18 jaguars to further test these
panels, which correctly recovered kinship relationships and allowed
inference of geographic origin of samples collected outside the spatial
scope of the original sample set. These results support the strong
potential of these panels as an efficient tool for application in
forensic, genetic, ecological, behavioral and conservation projects
targeting jaguars.