Getting to the core of the matter: Assessing the role of replication in sedimentary DNA metabarcoding

Replication plays a crucial role in experimental and sampling designs, enhancing statistical power and providing fine-scale data heterogeneity. Despite its significance, its impact remains underexplored in certain ecological and evolutionary contexts. This is particularly true for metabarcoding studies employing DNA extracted from sedimentary archives, where biological signals may assimilate ecological information via depositional and burial processes. These signals are frequently inferred from a solitary sediment core per site.

The current study aimed to assess the impact of diverse replication strategies within sedimentary DNA (sedaDNA) metabarcoding data, utilizing two genetic markers (mitochondrial COI and nuclear 18S) within a nested sampling framework. The experimental design encompassed three intertidal sites, with each site comprising three spatially distinct sediment cores, each representing a distinct biological replicate.

Additionally, two sediment depth horizons were sampled per core, and eight PCR (technical) replicates were taken for each sediment sample.

Variance partitioning analysis revealed that site identity and sediment age group accounted for approximately 70% of the variation in beta diversity. This suggests that among-site spatial variation and stratigraphic variation are the primary drivers of community composition. Conversely, variation among cores within a single site was minimal and statistically insignificant.