Field sampling guidelines for sedimentary ancient DNA (sedaDNA) research in lacustrine and coastal systems: from field collection to laboratory subsampling

Abstract

Sedimentary ancient DNA (sedaDNA) has emerged as a powerful proxy for reconstructing past biodiversity and environmental change in lacustrine and coastal systems, yet standardized field guidance remains limited, particularly for researchers working in tropical and coastal depositional environments. Here, we present a practical sampling framework covering the key field protocols of sedaDNA research, from field collection to laboratory subsampling, with emphasis on contamination control at each step. We review recent sedaDNA applications across multiple research fields, highlighting the growing interdisciplinary relevance of the technique. Particular attention is given to the challenges of DNA preservation in dynamic depositional environments, including coastal and semi-arid regions, where shallow, physically reworked sediments and recurring human disturbance amplify degradation and contamination risks. A Brazilian case study from Itapipoca, Ceará, illustrates how the absence of basic contamination precautions during excavation of Late Pleistocene megafaunal deposits produced metabarcoding results dominated by modern domesticated and synanthropic taxa, making the dataset uninterpretable for paleoecological reconstruction. Together, the guidelines and case study demonstrate that rigorous contamination control is not optional but essential to credible sedaDNA research, especially in tropical and coastal systems, environments that are scientifically underrepresented and increasingly threatened by anthropogenic change.

Keywords

Sedimentary ancient DNA (sedaDNA) / Contamination control / Sampling guideline / Tropical and coastal systems / Paleoecology

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