Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales

Abstract

Pangolins are among the most highly trafficked animals, with shipments of pangolin scales and products weighing several metric tonnes being seized at various ports. These large seizures are challenging to process and comprehensively genotype for both upstream provenance tracing and species identification for prosecution. In this study, we implemented a scalable DNA barcoding pipeline that leverages rapid DNA extraction and MinION sequencing to genotype a substantial proportion of scales subsampled from two record consignments seized in Singapore in 2019 (37.5 tonnes). This yielded a total of 2,346 cytochrome b (cytb) barcodes from white‐bellied (Phataginus tricuspis; 1,091 scales), black‐bellied (Phataginus tetradactyla; 227 scales) and giant (Smutsia gigantea; 1,028 scales) pangolin scales. Clustering analyses reveal rich haplotype diversity in the white‐bellied pangolin scales (121 haplotypes, 66 novel), while the genetic diversity of black‐bellied and giant pangolin scales appear more conserved (black‐bellied: 22 haplotypes, 15 novel; giant: 25 haplotypes, 21 novel). Using reference sequences, these scales could be matched to phylogeographical regions of origin. We find a large proportion of novel haplotypes likely from Western and Western Central Africa, suggesting potential resurgence of poaching and newly‐exploited populations in these regions. Our study illustrates the utility of extensively subsampling large seizures and outlines an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.This article is protected by copyright. All rights reserved

Fifteen years of extensive and inadvertent elasmobranch trade in Brazil detected by DNA tools

“…While Sanger sequencing is highly effective for accurate species identification, its continued high-cost for a large sample size poses challenges, particularly in resource-limited regions like Latin America, which can limit frequent market inspections. Several approaches can be pursued to address this such as, optimizing DNA sequencing protocols, including high-throughput techniques like amplicon sequencing, and exploring modern cost-effective methods, like real-time PCR and closed-tube DNA barcoding (Cardenosa et al, 2018;Ballard et al, 2020;Prasetyo et al, 2023;Yeo et al, 2023).…”