COI-Based DNA Barcoding of Pakistani Fauna: Progress, Challenges, and Future Directions Authors: Sohail Anjum, Ikram Ilahi, Qaiser Zaman, Muhammad Salman Khan, Rizwana Kousar, Ikram Ullah Journal: Journal of Animal and Plant Sciences (JAPS) ISSN: 1018-7081 (Print), 2309-8694 (Online) Volume: 36 Issue: 5 Year: 2026 DOI: https://doi.org/10.36899/JAPS.2026.5.0106 URL: https://doi.org/https://doi.org/10.36899/JAPS.2026.5.0106 Publisher: Pakistan Agricultural Scientists Forum Abstract:

DNA barcoding using the cytochrome oxidase I (COI) gene has revolutionized species identification and biodiversity research in Pakistan since 2006. This review assesses the progress, trends, and challenges of COI-based DNA barcoding in Pakistani fauna from 2006 to 2025. A total of 120 articles were downloaded, of which 91 were retained based on strict relevancy using PRISMA flow. Research efforts are unevenly distributed, with insects, particularly mosquitoes and fruit flies, receiving the most attention. However, mammals, amphibians, marine organisms, fungi, and microbes remain largely underrepresented. Geographic coverage and sample sizes vary widely, affecting statistical reliability and species representation. Methodological inconsistencies, such as unreported collection sites and varying trapping techniques, limit reproducibility and comparative analysis. Genetic divergence data reveal inconsistencies, with conspecific distances typically between 0-2% but sometimes reaching extreme values (e.g., 67.10%), suggesting sequencing errors, mislabeling, or reflecting data quality problems. Congeneric distances also vary significantly, emphasizing the need for taxon-specific barcoding thresholds. Phylogenetic analyses predominantly use MEGA software, with Neighbor-Joining and Maximum Likelihood methods being most common, while Bayesian inference remains underutilized, which provides statistical robustness and rate heterogeneity among models. The publication trend was slow from 2006 to 2012 but showed steady growth from 2013 to 2021 and a sharp rise from 2022 onwards, driven by increased funding and technological advancements. Research is mainly published in international journals, with some contributions to national journals such as the Pakistan Journal of Zoology. To enhance DNA barcoding in Pakistan, improvements such as expanded taxonomic and geographic coverage, standardized methodologies, increased data sharing, and integration with multigene approaches are necessary. Addressing these gaps will improve the accuracy and global relevance of COI-based DNA barcoding.

Keywords: DNA barcoding, COI gene, Biodiversity, Species identification, Pakistan fauna, Genetic divergence, Review