Data from: History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)
Data files
May 29, 2026 version files 460.94 MB
-
populations_complex_456.snps.vcf
33.76 MB
-
populations_HZ_7.snps.vcf
21.99 MB
-
populations_HZ_9.snps.vcf
79.62 MB
-
populations_HZwgri_8.snps.vcf
26.30 MB
-
populations_outgroups_2.vcf
284.30 MB
-
populations_wminiatus_3.snps.vcf
14.59 MB
-
README.md
2.69 KB
-
snapper_subspecies_110ind_beauti_jan2025.xml
365.72 KB
-
SNP_datasets_information.xlsx
12.18 KB
Abstract
Data associated with "History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)". The dataset includes genomic variant files (VCFs) that enable reanalysis under alternative filtering strategies, as well as an XML configuration file for reproducing phylogenetic analyses conducted using SNAPPER.
The VCF files contain genome-wide single nucleotide polymorphism (SNP) data derived from multiple Myioborus taxa, mainly corresponding to members of a young tropical Andes species complex (M. ornatus, and M. melanocephalus). These data is the base for analyses of population structure, spatial genetics and geographic cline analyses included in the paper. The included XML file contains model specifications and parameters required to replicate SNAPPER-based species tree analyses.
This dataset has broad reuse potential for studies of avian genomics, hybridization, and comparative phylogeography. Researchers may use these files to test alternative bioinformatic filtering pipelines, reproduce published analyses, or integrate the data into broader comparative datasets.
All scripts used to process data and conduct analyses are available on GitHub (https://github.com/lcespedesarias/myioborus-genomics). Raw data (fastq files) are available in the NCBI SRA.
Dataset DOI: 10.5061/dryad.msbcc2gck
Description of the data and file structure
Data from: History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)
Description of the data
This repository contains the genomic SNP datasets used to perform the analyses in the associated paper. The data genetic data was generated from tissue samples collected across the distribution of Myioborus ornatus and Myioborus melanocephalus. Laboratory procedures (ddRAD-seq) and bioinformatic pipelines are detailed in the Methods section of the manuscript.
The file numbering (e.g., _456, _9) corresponds to the SNP Dataset IDs listed in the SNP_datasets_information.xlsx table. This table contains the same information as the Supplementary Table 3 in the associated paper. Note that VCFs provided here correspond to the output of the populations program (STACKS): further filtering was performed prior to some analyses as explained in the SNP dataset information table. We also provide the .xml file used for the snapper analysis.
File Manifest
- populations_complex_456.snps.vcf: VCF file used for PCA, FST calculation, fineRADStructure, and Admixture (complex-wide analysis).
- populations_HZ_9.snps.vcf: VCF file used for triangulaR analyses (all SNPs from the hybrid zone assembly).
- populations_HZ_7.snps.vcf: VCF file used for hybrid zone-focused Admixture analysis.
- populations_HZwgri_8.snps.vcf: VCF file used for hybrid zone Admixture analysis including M. m. griseonuchus.
- snapper_subspecies_110ind_beauti_jan2025.xml: Input XML file for SNAPP/SNApper analysis, generated via BEAUti.
- populations_outgroups_2.vcf: VCF file used for RAxML-NG phylogenomic analysis (subsequently converted to NEXUS format as described in Methods).
- populations_wminiatus_3.snps.vcf: VCF file used for OrientAGraph analysis (subsequently converted to TreeMix format).
- SNP_datasets_information.xlsx: Excel file containing detail of SNP datasets (e.g., filtering parameters, number of samples included).
Access Information
Additional plumage data (plumage hybrid index), specimen metadata (locality, voucher numbers), and supplementary figures are available as Supporting Information through the journal's website.
Scripts to run analyses and additional files used to build figures (e.g. shapefiles) are available here: https://github.com/lcespedesarias/myioborus-genomics