Origins of adaptive genomic variation in a wild rodent
Data files
May 21, 2026 version files 1.16 GB
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phased_snps_for_tree_inference_neutral.zip
577.46 MB
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phased_snps_for_tree_inference_outliers.zip
579.26 MB
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README.md
1.64 KB
May 29, 2026 version files 1.16 GB
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phased_snps_for_tree_inference_neutral.zip
577.46 MB
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phased_snps_for_tree_inference_outliers.zip
579.26 MB
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README.md
2.43 KB
Abstract
Population history is a key yet underexplored determinant of local adaptation. Here, we assess its role by inferring the geographic origin of alleles at climate-associated loci. Using whole-genome data from 151 bank voles (Clethrionomys glareolus) sampled in Britain and four mainland European source populations with ancestry representing the Carpathian and Western refugia, we evaluated the origins of SNPs linked to climate adaptation at 1,074 candidate loci. This dataset includes regions of the genome 50kb upstream and downstream each of the 1,074 condidate loci which inferred to be in linkage disequilibrium with those candidate loci. We used those regions of the genome to infer the geographic origin of the alleles in the candidate loci by inferring haplotype trees. Most SNPs at adaptive loci represent widespread polymorphisms, shared across both European refugia and Britain. However, the larger and older Carpathian refugium contributed more unique SNPs associated with climate adaptation, which show a stronger positive correlation with high temperatures, compared to the smaller contribution of uniquely Western alleles. Together, these results demonstrate that local adaptation is shaped not only by shared ancestral variation but also the distinct evolutionary legacies of individual refugia.
Dataset DOI: 10.5061/dryad.k3j9kd5qq
Authors' full affiliations:
da Cruz, Marco 1,2; Marková, Silvia 3; Escalante, Marco 4; Searle, Jeremy 5; Kotlík, Petr 3; Lanier, Hayley 1,2
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK 73072
- School of Biological Sciences, University of Oklahoma, Department of Biology, University of Oklahoma, Norman, OK, USA
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Global Change Ecology and Evolution Research Group (GloCEE), Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853
Description of the data and file structure
Phased snps data in vcf.gz. Each of the 1074 files contains snps for different regions of the genome displaying 100,001 KB in length.
Files and variables
File: phased_snps_for_tree_inference_outliers.zip
Description: data set used to infer haplotype trees based on 1074 different regions of the genome of 100,001 kb each containing one outlier locus.
File: phased_snps_for_tree_inference_neutral.zip
Description: data set used to infer haplotype trees based on 1074 different regions of the genome of 100,001 kb each containing one outlier locus.
Code/software
Bash scripts used to infer haplotype trees. All the bash scripts can be executed using the command bash scriptname.sh. The description of each script (in italic) are in the order I executed them to run the analysis. The scripts for this analysis can be found in github: https://github.com/marcticruz/Origins-of-adaptive-genomic-variation-in-a-wild-rodent
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- the outlier loci was derived from: Marková, S., Lanier, H., Escalante, M., da Cruz, M.O.R., Horníková, M., Konczal, M., Weider, L., Searle, J., Kotlik P. 2023 Local adaptation and future climate vulnerability in a wild rodent. Nature Communications 14, 1–11.