Cundy, A. B. | Search bioRxiv

bioRxiv2026

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

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals may integrate ecological information through depositional and burial processes, and are often inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA (sedaDNA) metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S), under a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment depth horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained >70% of the variation in beta diversity, indicating that among-site spatial variation and stratigraphic variation were the dominant drivers of community composition. In contrast, variation among different cores within sites was small and non-significant (<5%). Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than among biological replicates and site identity, indicating limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may yield limited additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedaDNA metabarcoding datasets.

ecology↗

bioRxiv2025

Metabarcoding of sedimentary ancient DNA reveals centuries of species turnover and introductions of non-indigenous species in a highly urbanised estuary

Understanding how anthropogenic pressures shape ecosystems over time is crucial for managing both biodiversity and bioinvasion risk. Despite recent research efforts focussing on temporal community changes as a result of human impacts, little is known about such changes over periods exceeding a century. Here, we reconstructed long-term community changes and non-indigenous species (NIS) dynamics by using sedimentary ancient DNA (sedaDNA) metabarcoding and geochemical analysis of sediment cores samples collected from a temperate estuary (Southampton Water, southern British Isles) subject to significant human impacts for centuries. We detected 73 species of Metazoa and Plantae and classified them by their status (native, cryptogenic and NIS). Our results revealed sporadic detection of NIS (both failed and continuously successful NIS introductions) throughout the entire sedimentary record. Notably, some NIS were detected as early as the 18th century, indicating the presence of NIS introductions in pre-industrial times. We found a continuous overall decline in native species richness since the 19th century. In addition, we found distinct peaks in copper and zinc concentrations reflecting recent periods of intensified industrial and port activity, highlighting the role of human activities in shaping biodiversity patterns and NIS dynamics. Our findings demonstrate how metabarcoding of sedaDNA archives can reveal trends in the distribution of NIS and wider biodiversity over centuries. The integrated approach used here provides new insights into biodiversity changes through time, unravels key information for biodiversity conservation management and biosecurity policy, and shows the potential that sedaDNA metabarcoding has for investigating intrinsic attributes of NIS introductions.

ecology↗