Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective “evolve and resequence” natural experiments using sedaDNA. •Sequencing Late Pleistocene three-spined stickleback environmental genomes from sedaDNA•These genomes have a majority of marine-adapted ancestry at adaptive loci•Freshwater ancestry of large effect reflects findings from experimental releases•Sedimentary DNA can be used in retrospective “evolve and resequence” experiments Laine et al. sequence stickleback genomes from Late Pleistocene sediments of a post-glacial lake, which spans an ecological transition from marine to freshwater habitat. Most genes show marine ancestry; however, freshwater ancestry is found in loci of large effect size as early as the brackish phase, highlighting the chronology and tempo of adaptation.