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<p>We evaluated the performance of Oxford Nanopore Technologies (ONT) for high-throughput environmental DNA (eDNA) metabarcoding of carnivores in arid environments. Using ONT sequencing combined with the ONTbarcoder2 pipeline, we analysed pooled amplicons from 155 carnivore samples collected across Saudi Arabia, including tissue and non-invasive samples. The approach achieved a 98% success rate in recovering high-quality mitochondrial COI barcodes, exceeding standard barcode quality thresholds. Taxonomic assignment identified 149 carnivore samples representing six families, with 79% of sequences showing ≥ 99% identity to reference databases. As a case study illustrating the sensitivity of the method, DNA assigned to the Arabian leopard (<i>Panthera pardus nimr</i>) was detected from a fecal environmental sample. Phylogenetic analyses based on COI and 16S markers placed this sequence within the <i>P. pardus</i> clade, consistent with regional leopard lineages. Comparison with Sanger sequencing confirmed the high accuracy of ONT-derived barcodes (&gt; 99.9% identity). Our results demonstrate that ONT-based eDNA metabarcoding is an effective tool for rapid, non-invasive carnivore biodiversity assessment and has the potential to detect rare and elusive species. However, we emphasize that eDNA detection alone does not provide information on population size or persistence. This approach offers a complementary tool for biodiversity monitoring and conservation planning in regions where traditional surveys are challenging.</p>

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Assessing Oxford Nanopore-based eDNA metabarcoding for carnivore monitoring in Saudi Arabia: detection of Arabian leopard DNA as a case study

  • 期刊论文

  • 发表日期：

    2026年2月13日

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  • Abdulaziz N. Alagaili,
  • Nabil Amor

摘要

We evaluated the performance of Oxford Nanopore Technologies (ONT) for high-throughput environmental DNA (eDNA) metabarcoding of carnivores in arid environments. Using ONT sequencing combined with the ONTbarcoder2 pipeline, we analysed pooled amplicons from 155 carnivore samples collected across Saudi Arabia, including tissue and non-invasive samples. The approach achieved a 98% success rate in recovering high-quality mitochondrial COI barcodes, exceeding standard barcode quality thresholds. Taxonomic assignment identified 149 carnivore samples representing six families, with 79% of sequences showing ≥ 99% identity to reference databases. As a case study illustrating the sensitivity of the method, DNA assigned to the Arabian leopard (Panthera pardus nimr) was detected from a fecal environmental sample. Phylogenetic analyses based on COI and 16S markers placed this sequence within the P. pardus clade, consistent with regional leopard lineages. Comparison with Sanger sequencing confirmed the high accuracy of ONT-derived barcodes (> 99.9% identity). Our results demonstrate that ONT-based eDNA metabarcoding is an effective tool for rapid, non-invasive carnivore biodiversity assessment and has the potential to detect rare and elusive species. However, we emphasize that eDNA detection alone does not provide information on population size or persistence. This approach offers a complementary tool for biodiversity monitoring and conservation planning in regions where traditional surveys are challenging.