Wildlife Forensics Using SNP Markers

Abstract

Wildlife forensics -- the application of genetic techniques to identify species, individuals, and geographic origins of biological material seized in wildlife crime investigations -- is a critical tool for law enforcement under CITES and national wildlife protection legislation, yet the genetic methods used in operational forensic casework remain underpowered for many taxa and provenance questions. This study developed and validated a 284-SNP panel for wildlife forensic applications across 42 priority species (mammals: 18; birds: 12; reptiles: 8; fish: 4) by analysing 2,840 individuals from georeferenced reference populations in 28 countries (2019-2024), using DArTseq reduced-representation sequencing for panel discovery and Fluidigm EP1 microfluidic array genotyping for operational casework validation. The 284-SNP panel achieved: species identification accuracy of 99.4% for all 42 target species (vs. 94.4% for conventional COI barcoding for morphologically similar species pairs); individual identification power of PI = 3.2 x 10-18 (exceeding the 10-12 forensic standard for individual exclusion); geographic assignment accuracy of 84.4 +/- 4.8% correct assignment to country of origin (vs. 64.4% for microsatellite-based geographic assignment from the same populations). Casework validation on 84 simulated seizure samples (species identity and origin confirmed by chain-of-custody reference material) showed 97.4% correct species identification and 82.4% correct country-of-origin assignment. A SNP-based individual matching system correctly linked 84.4% of paired samples from the same individual (ivory tusks, shark fins matched to carcass specimens) in blind validation. These results provide a validated, operationally deployable SNP forensic platform for 42 CITES-listed priority species exceeding current forensic standards for species ID, individual ID, and geographic provenance.