Morphology-based preservation scoring predicts DNA detection success in elephant and mammoth ivory, bone, and teeth...

The illegal trade in elephant ivory and the legal use of mammoth ivory as a substitute continues to complicate detection and enforcement due to limitations in current identification methods. DNA-based approaches provide more definitive results compared to morphology-based or chemical-based methods, but are often costly and time-consuming. This study evaluated colorimetric loop-mediated isothermal amplification (LAMP) as a potential field-deployable alternative to quantitative PCR (qPCR) for detecting elephant and mammoth DNA from calcified tissues including ivory, bone, and teeth. We compared colorimetric LAMP with two qPCR assays. The longer amplicon assay targeted the same region as LAMP, and the shorter assay optimised for degraded DNA. qPCR amplicons were then sequenced using nanopore technology to achieve species and subspecies resolution. LAMP successfully amplified synthetic DNA but proved unsuitable for calcified tissue samples. The short-amplicon qPCR-sequencing workflow detected as few as 10 copies of elephant or mammoth DNA with high species-specificity. Nanopore sequencing further enabled subspecies resolution and resolved ambiguous qPCR results. The purpose-built WildSEQ analysis pipeline provided rapid, easily interpretable results, with lower computational requirements than standard BLAST workflows. Factors influencing detection success, including preservation state and sampling quantity, were explored. A simplified preservation scoring system based on easily observable morphological traits (colour, brittleness, structural condition) was developed to predict the likelihood of amplifiable DNA being present prior to destructive sampling. Total preservation score strongly predicted DNA detection success, with colour identified as the simplest and most useful indicator. Sample quantity (mg) was also a strong predictor of successful species identification regardless of preservation state. This simplified and integrated workflow combines qPCR sensitivity with nanopore sequencing resolution for species identification from calcified tissues. The use of preservation scoring shows promise as a rapid, non-destructive tool to support evidence-based decision making in wildlife forensic science and ancient DNA applications.