Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation
Cite this dataset
Foote, Andrew (2024). Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation [Dataset]. Dryad. https://doi.org/10.5061/dryad.z8w9ghxkj
Abstract
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.
README: Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation
https://doi.org/10.5061/dryad.z8w9ghxkj
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, <=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
Funding
European Research Council, Award: 101045346-EXPLOAD, Horizon Europe COG-2021
The Research Council of Norway, ERC Support Grant