Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)

Crescent butterflies of the Phyciodes tharos group have a long-standing reputation for taxonomic difficulty. We assessed species boundaries in the P. tharos group using genome-wide SNP data, focusing on sampling in western Canada where four species (P. tharos, P. cocyta, P. pulchella, and P. batesii) have classically been recognized. Phylogenetic and cluster-based analyses confirm that there are indeed four species based on the maintenance of genomic integrity in the presence of occasional hybridization and low levels of gene flow. Mitochondrial COI does not consistently distinguish species, with haplotypes extensively shared between species. Here, we provide data matrices and tree files from the phylogenetic and cluster-based analyses., , , # Data from: Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)

[https://doi.org/10.5061/dryad.q83bk3jq6](https://doi.org/10.5061/dryad.q83bk3jq6)

Data matrices and tree files for phylogenetic analyses of SNP & COI data, and data matrix for cluster-based analyses of SNP data. The SNP tree, STRUCTURE, and PCA results supported the existence of four traditionally recognized species in the *Phyciodes tharos* species group, in the province of Alberta, Canada. Phylogenetic analysis of COI sequences demonstrated that COI is not a reliable marker for identification in this group.

## Description of the data and file structure

COI phylogenetic analysis
Phyciodes_COI.nex

Phylogenetic SNP analysis
Phyciodes_SNP_phylogeny_156ind_50md.vcf

Data matrix of 2443 SNPs (2130 informative SNPs) for 156 Phyciodes individuals.
Filtered to <50% missing data and <5% minor allele frequency for phylogenetic analysis.
Phyciodes_SNP.nex

Data matrix of...