A Roadmap for Using Hybridisation Capture–BasedTarget Enrichment of Ancient Environmental DNA in Palaeoecology

This review provides a practical roadmap for applying hybridisation capture to ancient environmental DNA (eDNA), a rapidly developing technique that enables researchers to recover rare and degraded genetic signals from sediments, ice and other environmental archives. The authors explain how targeted enrichment using specially designed DNA or RNA “baits” can overcome the limitations of conventional metabarcoding and shotgun sequencing by selectively isolating low-abundance DNA from plants, animals and other organisms that would otherwise be difficult or impossible to detect. Drawing on recent case studies, the paper demonstrates how hybridisation capture has successfully reconstructed past ecosystems, tracked species distributions, recovered ancient genomes and revealed biodiversity changes across timescales ranging from thousands to millions of years. It also outlines best practices for bait design, laboratory protocols, data analysis and reporting standards, while highlighting current challenges and future opportunities. As ancient eDNA becomes an increasingly important tool in palaeoecology, the review provides essential guidance for researchers seeking to use targeted enrichment approaches to better understand long-term environmental and ecological change.

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