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.