Bioinformatics-Driven Environmental DNA Metabarcoding and Conservation Genomics for Non-Invasive Wildlife Biodiversity Monitoring under Climate Change

Abstract

Global biodiversity is declining rapidly as anthropogenic climate change interacts with habitat loss, disease emergence and overexploitation to reshape species distributions and population viability. Conventional survey methods, including live trapping, visual census and invasive tissue sampling, are frequently slow, costly and disturbing to the organisms under study, so they cannot keep pace with the scale at which ecosystems are now changing. Environmental DNA (eDNA) metabarcoding, supported by conservation genomics and modern bioinformatic pipelines, offers a non-invasive alternative capable of detecting entire assemblages of organisms from water, soil, air, sediment and even surface swabs. This review synthesises recent methodological and empirical literature to examine how bioinformatics-driven eDNA metabarcoding and population genomic tools are being integrated for wildlife biodiversity monitoring under a changing climate. It traces the workflow from sample collection through amplicon and shotgun sequencing to taxonomic classification, highlighting the computational tools, reference databases and quality control steps that determine the reliability of biodiversity inferences. It then considers how population genomic approaches complement eDNA surveys by estimating effective population size, inbreeding, adaptive potential and demographic history in threatened species. Case studies spanning critically endangered birds, marine reptiles, river ecosystems, airborne biomonitoring and disease surveillance in migratory waterfowl illustrate the practical reach of these tools. The review closes by discussing persistent limitations, including reference database incompleteness, taxonomic classifier disagreement, degradation of DNA under variable environmental conditions, and the computational capacity gap faced by many biodiversity-rich but resource-limited regions, before outlining priorities for standardisation and capacity building relevant to zoological research in Pakistan and other developing regions.