Banos, E. | Search bioRxiv

bioRxiv2026

SedaDNA metabarcoding reveals hidden histories of within-species sequence variation

Most genetic data come from contemporary populations, leaving historical changes in within-species variation poorly documented. Sedimentary ancient DNA (sedaDNA) offers an opportunity to recover historical sequence variation, but its potential to reconstruct temporal changes in within-species composition remains underexplored. Here, we analysed dated sediment cores from eight Atlantic and Mediterranean coastal wetlands using COI and 18S metabarcoding, treating amplicon sequence variants as putative haplotypes. Across native, non-indigenous and cryptogenic taxa, accumulated haplotype diversity and geographic sharing varied markedly among species and markers, without consistently distinguishing species status. Temporal reconstructions revealed that accumulated haplotype networks combined distinct sets of variants detected across historical periods. Broader analyses of 18S data further showed substantial variation in haplotype composition among periods, sites and taxa. By resolving the temporal and spatial distributions of within-species sequence variants, our findings demonstrate how sedimentary DNA archives can uncover historical dimensions of biodiversity obscured by time-aggregated analyses, establishing a foundation for historical metaphylogeography.

evolutionary biology↗

bioRxiv2026

Long-term biodiversity responses to anthropogenic change are spatially and taxonomically heterogeneous across coastal wetlands

Coastal wetlands have undergone centuries of anthropogenic modification, yet their long-term biodiversity trajectories remain poorly understood because ecological monitoring rarely extends beyond recent decades. Sedimentary ancient DNA (sedaDNA) offers a historical perspective for evaluating how biodiversity patterns vary across environmental contexts and timescales. We combined COI and 18S sedaDNA metabarcoding with 210Pb and radiocarbon chronologies, sediment geochemistry and stable-isotope records from eight coastal wetlands across four regions of the Iberian Peninsula. We reconstructed changes in eukaryotic amplicon sequence variant (ASV) richness and taxonomic composition and examined their relationships with an Anthropogenic Enrichment Index (AEI) based on ten elements potentially associated with human activities. Richness-AEI relationships differed among sediment records and genetic markers. Higher enrichment was associated with lower richness for both markers in one Cadiz record, whereas COI richness increased with enrichment in the Ebro Delta. However, after accounting for calendar time, only the positive association in the Ebro Delta remained statistically significant, indicating that several initial relationships were partly explained by shared temporal trends. Exploratory rolling correlations further suggested that the direction of richness-enrichment associations varied across historical periods within individual records. Taxonomic profiles differed between markers and wetlands, while community composition was strongly differentiated among sediment records, highlighting ecological variation not captured by richness alone. Multiproxy changes also followed locally specific configurations rather than a common regional trajectory. Together, these findings show that long-term relationships between sedimentary enrichment and biodiversity are context-dependent and sensitive to the temporal perspective considered. Integrating molecular, geochemical and isotopic records can therefore improve the historical interpretation of biodiversity change and inform conservation approaches that account for taxonomic composition, environmental history and locally appropriate reference conditions.

ecology↗