Targeted sequencing enhances detection of pangolin trafficking hotspots and dynamics of both domestic and global trade markets.

Pangolins have become emblematic of the global wildlife trade crisis due to intense trafficking for consumption and traditional medicine. Coupled with habitat loss, the illicit trade in pangolins has severely threatened wild populations. Genetic identification of distinct pangolin populations is an imperative step toward guiding effective and informed conservation management. These populations can serve as a reference for assigning seized individuals to their geographic origins, and thus tracing trafficking networks. However, pangolin population genetics studies have been hindered by limited sampling of geo-referenced individuals, largely due to the species' elusive nature. To address this, we developed a tailored gene-capture approach targeting 671 loci totaling 627 kb with high evolutionary and adaptive value across all eight pangolin species. We optimized the approach for low-quality DNA, including samples from museum collections and wildlife trade, such as bushmeat and scale seizures. We reassessed range-wide population delineations for the three most traded species, the white-bellied (Phataginus tricuspis), Sunda (Manis javanica), and Chinese (M. pentadactyla) pangolins, highlighting the need for biogeographically consistent lineage nomenclature and spatially aware analyses to support coherent conservation planning. The unprecedented geo-referenced DNA database for the three species yielded snapshot insights into pangolin trafficking hotspots and trade dynamics of both domestic markets and global trade seizures, the former providing novel insights into bushmeat trade. Domestic trade reflects local and occasional cross-border sourcing, averaging 454 km across the three species, while international trafficking seizures in mostly scales point to broader, regional procurement. However, common sourcing regions between the two trade market types indicate their interconnectivity, suggesting that local trade may contribute to international trade supply. Our study identified significant international trade hotspots for the white-bellied, Sunda, and Chinese pangolins, centered around southwestern Cameroon, southwestern Borneo Island, and Myanmar, respectively. Addressing geo-referenced sampling gaps and increasing local-to-global seizure data over time may offer deeper spatiotemporal insights into pangolin trade dynamics. Our study design may serve as a replicable model for enabling authorities and practitioners to implement intelligence-driven, geographically targeted interventions, by identifying the key regions most implicated in pangolin trafficking.