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 aDNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms, and to thereby potentially provide an understanding of the evolutionary histories of past populations. To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than one gram of sediment. Here we maximise sequence coverage by extracting DNA from ~50x more sediment per sample than the majority of previous studies, 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 threespine stickleback at key time points of this transition. We find a staggered temporal dynamic, in which freshwater alleles ..., , , # Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

## Metadata accompanying the study by Laine et al. Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.

#### **Post-mortem damage patterns**

**Files Andy_metaDMGout.csv:** The output of Metadamage performed on paired-end sequencing data from individual layers from three sediment cores extracted from Jossavannet lake, Finnmark, Norway, generated across a run of a Novaseq S4 lane.

**File Damage_patterns_shotgun_collapsed_reads.pdf:** Post-mortem damage plots of collapsed reads of sequence data from sediment layers and bones mapped to the stickleback reference genome GasAcu1.0

#### **Capture bait design details and sequences**

**File input-seq.fas:** 10,149 SNP coordinates were extended in both directions to reach a 121 nucleotide window to extract target sequences. There is a total target size of 1,228,029 nucleotide and an average GC co...