Genomic divergence and introgression between cryptic species of a widespread North American songbird

Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulated evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic v..., Genetic samples were collected from the field and museum specimens. DNA was extracted from samples and used to prepare GBS (genotyping-by-sequencing; Elshire et al. 2011) libraries for sequencing. Sample information can be found in the supplementary materials of our manuscript. We have also included an example bioinformatic script for data processing along with the initial VCF file of SNPs prior to any filtering. , , # Genomic divergence and introgression in a cryptic species complex: Scripts and VCF file

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This data archive contains:
\- In the file Askelson\_etal\_bioinformatics\_v2\.txt : a bioinformatic script example to show how the data was processed\. 
\- In the file adapter\_files\_trimming\.zip: A zip file of \.fa files that were used to trim adapters from reads in Trimmomatic\.
\- In the file wbnu\_plate1to5\_411\_variants\_wholegenome\.vcf\.gz : a compressed VCF file with SNP information from each of the samples used in the study\. This VCF file is the initial output of SNP calling without any filtering\.

## Description of the Data and file structure

The VCF file contains SNP (single nucleotide polymorphism) data for each sample. This is an unfiltered file with unphased genotypes. \"./.\" indicate missing data in the VCF. 
Our script shows how the data was processed and has comments in the file describing the steps. These programs were used on Digital Research Alliance of Canada compu...