Data from: Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)
Data files
Mar 14, 2024 version files 20.24 MB
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Phyciodes_COI.contree
21.26 KB
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Phyciodes_COI.nex.nex
142.17 KB
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Phyciodes_SNP_50MR.tre
14.45 KB
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Phyciodes_SNP_phylogeny_156ind_50md.vcf
12.04 MB
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Phyciodes_SNP_popgen_152ind_20md.vcf
7.62 MB
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Phyciodes_SNP.contree
7.85 KB
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Phyciodes_SNP.nex.nex
387.98 KB
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README.md
1.99 KB
Abstract
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.
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 2443 SNPs (2130 informative SNPs) for 156 Phyciodes individuals.
In IUPAC format, created from the vcf file.
Phyciodes_SNP.contree
Maximum likelihood consensus tree of 2130 informative SNPs for 156 Phyciodes individuals.
Produced from the Nexus file using IQ-TREE 2.0.7 and the built-in ModelFinder which selected GTR+F+R5.
Ultrafast bootstrap values (2000 iterations) are included as “label”.
Phyciodes_SNP_50MR.tre
Maximum likelihood 50% majority rule consensus tree.
Nodes with <50% UFBootstrap support in the Phyciodes_SNP.contree file were collapsed to make this file.
Population genetics SNP analyses
Phyciodes_SNP_popgen_152ind_20md.vcf
Data matrix of 1477 SNPs for 152 Phyciodes individuals.
Filtered to <20% missing data and <5% minor allele frequency for population genetics analyses.
Sharing/Access information
Raw fastq files containing genomic SNP data are deposited on NCBI SRA as BioProject PRJNA1032909.
COI sequences are deposited on GenBank as accessions OR896666-OR896818.