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Abstract

Ancient DNA has revolutionised our understanding of the evolutionary histories of past and present-day populations. The sampling of bones, coprolites, seeds, skin and teeth of ancient animals and plants have provided key insights into adaptation, demographic history and extinction. However, individual samples typically provide a snapshot in time. In contrast, time series of ancient DNA that span demographic, ecological and evolutionary change can provide novel insights into the chronology and tempo of evolutionary processes. The advent of sedDNA as a tractable source of genome-scale data offers a potential source of time-series of genomic change. To date, time series in ecosystem biodiversity have been reconstructed from sedDNA, typically using DNA metabarcodes or shotgun sequence data generated from less than 1 gram of sediment. Here we increase sequence coverage by processing two orders of magnitude more sediment per sample than previous studies, which provided genotype resolution results. Reconstructing a time-series of environmental genomes from Late Pleistocene sedDNA we track adaptive genotypes of threespine stickleback (Gasterosteus aculeatusacross) during the ecological change from marine to freshwater. We find rapid adaptation at known loci of large effect, e.g. EDA. Our findings open up new avenues to explore the temporal context of past evolutionary processes.