Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca)

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 th..., From a dataset of 58 complete jaguar genomes from Brazil (Sartor et al. [in prep]), we used a genotype likelihood approach to identify 13,373,949 SNPs, that were later filtered according to their coverage, depth, mapping quality, missing data, minor allele frequence, linkage disequilibrium, repetitive regions and Hardy-Weinberg Equilibrium. With the remaining 83k SNPs, we grouped individuals according to their biomes of origin (Amazon: n=18; Atlantic Forest: n=14; Cerrado: n=14; Caatinga: n=6; Pantanal: n=6) and calculated pairwise FST values between biomes.
To select the most informative sites for geographic assignment, we ranked the 83k SNPS based on their pairwise FST values (from highest to lowest) between the sampled biomes and kept the 50 loci with the highest FST from each pairwise comparison. We identified a panel comprising 459 SNPs. This set included the top 50 SNPs of each pairwise biome comparison; 41 SNPs were retrieved in more than one comparison and were ke..., , # Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca)

**Paper:** Development of a SNP panel for geographic assignment and population monitoring of jaguars (*Panthera onca*)

This README file describes the data accompanying the above publication.

### **Description**

The present panel comprises jaguar genotypes from 459 highly informative SNPs for geographic traceability, individual identification and kinship, and another 8 sex-linked SNPs for sexing. These SNPs were identified and selected from a dataset of 58 complete jaguar genomes from Brazil, mapped against the chromosome-length genome assembly generated by the DNA Zoo team (GCF_028533385.1).

### Files

**1** - The CSV file named as **\"Jag-SNPpanel_coordinates_and_genotypes.csv\"** contains:

* ID_SNP: SNP identifier.
* CHROM:POS: Scaffold identification and SNP position, based on the reference genome.
* Allele1/Allele2: Information about the reference alleles (Allele1) and alt...,