RAD-seq vcf files for the leaf beetle Gonioctena quinquepunctata sampled across Europe
Data files
Jul 11, 2025 version files 9.26 MB
Abstract
The data set was created to characterize genetic variation in a montane leaf beetle, Gonioctena quinauepunctata, whose current range spans several mountains in Europe, and to compare alternative hypotheses about its evolutionary history in response to climate changes that occurred at the end of the Quaternary.
https://doi.org/10.5061/dryad.ht76hdrs8
Description of the data and file structure
Samples of Gonioctena quinquepunctata were collected in the Alps, Vosges, Massif Central and Pyrenees. A RAD-seq strategy was used to genotype all samples. DNA sequences were analyzed with Stacks v. 2.62. Two vcf data sets were generated, keeping only SNPs for which we could call a genotype for 50% of the samples separately for each mountain range. The first vcf data set (Gquinquepunctata_RADseq_phylogeography_R50_allsnp.vcf.gz) contained all retained SNPs, while the second data set (Gquinquepunctata_RADseq_phylogeography_R50_randomsnp.vcf.gz) contained only one SNP per locus, which was randomly selected for each locus.
Files and variables
File: Gquinquepunctata_RADseq_phylogeography_R50_randomsnp.vcf.gz
Description: Contains one randomly selected SNP per locus for which we had a genotype for at least 50% of the samples per mountain range
File: Gquinquepunctata_RADseq_phylogeography_R50_allsnp.vcf.gz
Description: Contains all SNPs for which we had a genotype for at least 50% of the samples per mountain range
Sampling locations can be deduced from sample names: they correspond to the first 4 letters of the locations listed in Table S3 of the associated manuscript.
Code/software
The data sets are in the standard vcf format and were created with the STACKS software.
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- N/A
Samples of Gonioctena quinquepunctata were collected in the Alps, Vosges, Massif Central and Pyrenees. A RAD-seq strategy was used to genotype all samples. DNA sequences were analyzed with Stacks v. 2.62. Two vcf data sets were generated, keeping only SNPs for which we could call a genotype for 50% of the samples separately for each mountain range. The first vcf data set (Gquinquepunctata_RADseq_phylogeography_R50_allsnp.vcf.gz) contained all retained SNPs, while the second data set (Gquinquepunctata_RADseq_phylogeography_R50_randomsnp.vcf.gz) contained only one randomly selected SNP per RAD sequence (locus).