Targeted sequencing enhances detection of pangolin trafficking hotspots and dynamics of both domestic and global trade markets
Pangolins are among the most trafficked mammals globally, facing critical threats from illegal wildlife trade and habitat loss. Effective conservation of wild pangolin populations requires the ability to genetically identify distinct lineages and trace the origins of seized individuals.   To address this, we developed and applied a targeted gene-capture sequencing approach optimised for low-quality DNA, such as that from confiscated and museum specimens. Our bait set was designed to target genomic regions of high evolutionary and adaptive value across all eight extant pangolin species. Using this approach, we generated population-level genomic data for over 700 individuals, with a focus on the three most heavily traded species: the white-bellied (Phataginus tricuspis), Sunda (Manis javanica), and Chinese pangolins (Manis pentadactyla).  We present a comprehensive, geo-referenced population genomics dataset spanning the range of these species, providing new insight into biogeographic population structure. Our findings reveal distinct regional trade patterns and highlight several international trafficking hotspots. Moreover, we detect overlap in the sourcing patterns of domestic and international trade, indicating that localised markets may feed into global trafficking networks.  This dataset enhances our understanding of pangolin population structure, informs targeted interventions, and offers a framework for the future integration of seizure data into conservation planning.   These data support the publication: Heighton et al. (in press), "Targeted sequencing enhances detection of pangolin trafficking hotspots and dynamics of both domestic and global trade markets". The gene-capture bait references (.fasta) used to design the baits and map the raw reads from this study can be found here: https://doi.org/10.5281/zenodo.19286247.