Processed ddRAD SNP dataset and metadata for: Panmixia in a widespread butterfly: High dispersal and ecological generalism buffer against landscape fragmentation
Data files
Sep 11, 2026 version files 2.13 MB
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excluded_individuals.txt
421 B
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metadata.praphe.xlsx
30.58 KB
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p_rapae_final_filtered_snps.vcf.gz
2.03 MB
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p_rapae_final_filtered_snps.vcf.gz.tbi
68.50 KB
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README.md
4.61 KB
Abstract
Habitat fragmentation is widely expected to reduce population connectivity and increase genetic differentiation, although the strength of these effects depends on species-specific traits such as dispersal ability. Here, we investigated the population genetic structure of the cosmopolitan butterfly, Pieris rapae L. (Lepidoptera: Pieridae), across western Germany using genome-wide single-nucleotide polymorphism (SNP) data. To analyze the effects of landscape structure on genetic connectivity, we applied a paired study design comprising four landscape pairs, each consisting of a highly intensified, modern agricultural landscape and a more heterogeneous, traditional landscape. Our results revealed no evidence of genetic differentiation. Pairwise FST values were close to zero; we detected no isolation by distance, and clustering analyses supported a single genetic population. No meaningful associations between genetic variation and environmental variables were detected, with landscape effects explaining less than 0.4% of genomic variation. Consequently, we found no evidence for stronger genetic structuring in modern compared to more connected traditional landscapes. Our results suggest that extensive habitat fragmentation does not necessarily translate into reduced genetic connectivity in highly mobile, generalist species. In P. rapae, high dispersal ability and ecological generalism appear to buffer against the genetic consequences of landscape modification, resulting in panmictic population structure even across strongly contrasting agricultural landscapes.
Dataset DOI: 10.5061/dryad.g79cnp65w
Description of the data and file structure
This dataset contains processed double-digest RAD sequencing (ddRAD-seq) data and associated metadata used to investigate population genomic structure, dispersal, and connectivity in the cabbage white butterfly, Pieris rapae. Individuals were sampled across fragmented landscapes and sequenced to assess whether high dispersal ability and ecological generalism buffer populations against the genetic effects of habitat fragmentation. Raw sequencing reads were generated for 640 individuals and archived in the NCBI Sequence Read Archive (SRA). After quality filtering based on missing data, coverage, and relatedness/coancestry, 596 individuals and 10,997 SNPs were retained for downstream analyses. The files deposited here correspond to the final filtered dataset used in the analyses presented in the manuscript.
Files and variables
File: p_rapae_final_filtered_snps.vcf.gz
Description
Compressed VCF file containing the final filtered SNP dataset used in downstream analyses (596 individuals, 10997 SNPs).
File: p_rapae_final_filtered_snps.vcf.gz.tbi
Description: Tabix index file forp_rapae_final_filtered_snps.vcf.gz, enabling rapid access to compressed VCF records.
File: metadata.praphe.xlsx
Description: Metadata for the 596 retained individuals included in the final filtered SNP dataset. Each row corresponds to one individual retained for downstream analyses
Variables
· sampleID: unique sample identifier matching sample names in the VCF file (e.g., GW_1.10).
· population: sampling population identifier.
· Plot: plot identifier within sampling locality.
· coordinates: geographic coordinates of sampling location.
· type: habitat or land-use category associated with the sampling site.
· poppair: paired population comparison category used in downstream analyses.
· Within_pair_distance: geographic distance within population pair (km).
File: excluded_individuals.txt
Description: List of 44 individuals excluded from downstream analyses after filtering for missing data, coverage, and relatedness/coancestry
Variables
- sample_name: unique sample identifier corresponding to excluded individuals (e.g., GW_1.8).
Missing values: none.
Code/software
The primary processed dataset is provided as a compressed Variant Call Format file (p_rapae_final_filtered_snps.vcf.gz), which can be viewed and processed using standard genomics software such as bcftools (v1.18 or later), vcftools (v0.1.16 or later), or R packages including vcfR and adegenet. The accompanying index file (.tbi) enables rapid access to VCF records using tabix-compatible tools.
Metadata are provided in Microsoft Excel format (.xlsx) and can be viewed in spreadsheet software such as Microsoft Excel, LibreOffice Calc, or imported into R/Python.
The VCF dataset was generated from a filtered PLINK dataset using PLINK v1.9 (Purcell & Chang). Downstream population genomic analyses were performed in R (v4.x), including multivariate analyses using packages such as adegenet. Sample metadata and excluded sample lists are provided in standard tabular formats and require no specialized software beyond spreadsheet or text editors.
Access information
Other publicly accessible locations of the data:
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Raw sequencing reads are publicly archived in the NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1462033 and will be accessible at:
https://www.ncbi.nlm.nih.gov/sra/PRJNA1462033This Dryad dataset contains the processed SNP dataset and associated metadata used in downstream analyses.
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Data were derived from the following sources:
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Processed SNP data were derived from raw double-digest RAD sequencing (ddRAD-seq) reads generated for this study and mapped to the publicly available Pieris rapae reference genome from NCBI GenBank. Raw sequence reads generated in this study are deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1462033. No third-party proprietary datasets were used.
Reference genome source: NCBI GenBank (Pieris rapae reference assembly; public domain / NCBI data access terms).
