DOI: 10.5061/dryad.9p8cz8wm0
title: Genomic divergence and introgression between cryptic species of a widespread North American songbird

description: 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
 variation of over 300,000 loci revealed four highly differentiated
 populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n =
 138; and Rocky Mountains South, n = 150) with geographic ranges that are
 adjacent. We observed a moderate degree of admixture between Rocky
 Mountain populations but only a small number of hybrids between the
 Rockies and the Eastern population. The rarity of hybrids together with
 high levels of differentiation between populations is supportive of
 populations having some level of reproductive isolation. Between
 populations, we show evidence for introgression from a divergent ghost
 lineage of white-breasted nuthatches into the Rocky Mountains South
 population, which is otherwise closely related to Rocky Mountains North.
 We conclude that white-breasted nuthatches are best considered at least 3
 species and that ghost lineage introgression has contributed to
 differentiation between the two Rocky Mountain populations. White-breasted
 nuthatches provide a dramatic case of morphological similarity despite
 high genomic differentiation, and the varying levels of reproductive
 isolation among the four groups provide an example of the speciation
 continuum. 
description: 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. 
description: # Genomic divergence and introgression in a cryptic species complex:
 Scripts and VCF file *** 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 computing resources.