Data from: Genetic depletion does not prevent rapid evolution in island-introduced lizards
Data files
Oct 30, 2023 version files 8.77 MB
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README.md
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Sherpa_et_al_2023_Datasets.zip
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Sherpa_et_al_2023_ECE_pop_map.txt
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, Pod Mrčaru), including the islet of Pod Mrčaru where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated to a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction, and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci, and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
README
Data from: Genetic depletion does not prevent rapid evolution in island-introduced lizards
https://doi.org/10.5061/dryad.rxwdbrvg2
Authors: Stéphanie Sherpa, Josephine R. Paris, Iolanda Silva-Rocha, Viola Di Canio, Miguel Angel Carretero, Gentile Francesco Ficetola, Daniele Salvi
Journal: Ecology and Evolution
Experiment
Double digest restriction associated DNA sequencing (ddRADseq)
Description of the data and file structure
Sample information; file: Sherpa_et_al_2023_ECE_pop_map.txt
Datasets; file: Sherpa_et_al_2023_Datasets.zip; include:
(1) SNP dataset after filtering for missing data, low sequencing coverage, and excess of shared heterozygosity (all SNPs; minor allele count = 1)
VCF file: N=24 individuals; 329,673 SNPs distributed over 82,404 loci; file: Sherpa_et_al_2023_ECE_full_SNP_dataset.vcf
(2) SNP dataset used for preliminary population structure analysis (1 random SNP per locus; minor allele count = 3)
VCF file: N=24 individuals; 54,050 SNPs; file: Sherpa_et_al_2023_ECE_SNP_dataset_popgen_1.vcf
subsequent datasets after removing one highly admixed individual in MRC
(3) Datasets used for selection analysis (1 random SNP per locus; minor allele count = 3)
BayeScan file: N=23 individuals; 52,499 SNPs; file: Sherpa_et_al_2023_ECE_SNP_dataset_bayescan.txt (not imputed)
Pcadapt file (LFMM format): N=23 individuals; 52,499 SNPs; file: Sherpa_et_al_2023_ECE_SNP_dataset_pcadapt.lfmm (missing genotypes imputed by the median locus genotype among individuals)
subsequent datasets after removing outlier loci from the SNP dataset
(4) SNP dataset used for analysis of low-frequency polymorphisms (1 random SNP per locus; no MAF filter)
VCF file: N=23 individuals; 73,847 SNPs; file: Sherpa_et_al_2023_ECE_SNP_demography.vcf
(5) SNP dataset used for analyses of population structure and genetic diversity (1 random SNP per locus; minor allele count = 3)
VCF file: N=23 individuals; 52,470 SNPs; file: Sherpa_et_al_2023_ECE_SNP_dataset_popgen_2.vcf
Sharing/Access information
Individual sequences (demultiplexed paired-end fastq files) are available in the European Nucleotide Archive repository (http://www.ebi.ac.uk/ena; project accession PRJEB65979).
Sample accession numbers are provided in the pop map file.