COI-Based DNA Barcoding in Pakistan: Progress, Challenges, and Future Directions

Abstract DNA barcoding using the cytochrome oxidase I (COI) gene has revolutionized species identification and biodiversity research in Pakistan since 2006. This review evaluates the progress, trends, and challenges of COI-based DNA barcoding across various taxa, focusing on taxonomic coverage, genetic divergence, sampling methodologies, publication trends, and phylogenetic analyses. A total of 120 articles were downloaded, of which 91 were retained based on strict relevancy. Research efforts are unevenly distributed, with insects, particularly mosquitoes and fruit flies, receiving the most attention, followed by economically significant freshwater fish like Cyprinidae. However, mammals, amphibians, marine organisms, fungi, and microbes remain largely underrepresented, highlighting the need for broader taxonomic studies. 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 cryptic species or sequencing errors. Congeneric distances also vary significantly, emphasizing the need for taxon-specific barcoding thresholds instead of a universal cutoff. Phylogenetic analyses predominantly use MEGA software, with Neighbor-Joining and Maximum Likelihood methods being most common, while Bayesian inference remains underutilized. The publication trend was slow from 2006 to 2012 but showed steady growth from 2013 to 2021 and a sharp rise from 2022 onwards due to increased funding and technological advancements. Research is mainly published in international journals, with some contributions in national journals like 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, supporting better conservation and sustainable management of Pakistan’s biodiversity.