DOI: 10.5061/dryad.z8w9ghxkj
title: Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

description: 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 at known loci of large effect in marine-freshwater divergence of
 threespine stickleback (e.g. EDA) were already established during
 the brackish phase of the formation of the isolation basin. Yet 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 threespine sticklebacks at the end of the
 last glacial period complements contemporary experimental approaches and
 highlights the untapped potential for retrospective
 ‘evolve-and-resequence’ natural experiments using sedaDNA.
description: # 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 content of 42.2%. Targets
 were soft masked for simple and low complexity repeats against vertebra
 database. Strings of N's up to 10 nucleotides were replaced with T.
 **File baits-4perSNP.fas:** 40,596 raw baits designed using 60 nucleotide
 probes. There are 4 probes per SNP, 2 overlapping baits per (1 for each
 allele), and 2 that flank the SNP (1 directly upstream and 1 directly
 downstream of the SNP). **File Bait-Screening_BLAST_analysis_(1).pdf:**
 Information regarding BLAST filtration **File
 baits-Moderate-25RM-noMito.fas:** 38,391 baits passed Moderate BLAST
 filtration, &lt;=25 softmasked for repeats, and no blast hits to the
 over-represented mitochondrial genome. **File Baits-per-Target.txt:**
 There are 10,026 unique targets represented in the filtered file. 9,177
 targets retained all 4 probes designed, 384 with 3 probes retained, 66
 targets with 2 probes retained, and 399 targets have 1 probe retained.
 **File NTNU-baits-4perSNP-filtration.txt:** output of the BLAST analysis
 performed #### **Metagenomic Analyses** **Files
 'sediment_layer'.txt:** Competitive mapping to RefSeq Mitogenome
 Database results