Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation

When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z..., Sample Collection
For this project, we collected blood samples for genomic analysis from individuals of wild Z. leucophrys and Z. atricapilla in south-western British Columbia. The dataset includes a metadata file in .csv format, with locality, date and time of collection, measurements, barcodes, etc. associated with all samples.
The first round of fieldwork was conducted at the Iona Island Bird Observatory (IIBO) in Richmond, British Columbia, in Spring 2019. Birds were captured passively in mist nets and banded as part of the station’s normal migration monitoring operations. We then took 10–40 μL of blood from the brachial vein of each bird of the target species and stored these samples in 500 μL of Queen’s Lysis Buffer (Seutin et al., 1991). We measured wing chord, tail length, tarsus length, mass, culmen length, beak depth, and beak width. A total of 19 Z. atricapilla and 14 Z. leucophrys of indeterminate subspecies were sampled during this initial period.
The second round of field ..., The metadata file is in .csv format, which can be opened in any text editor.
The files containing scripts used to process samples are in .txt format and can be opened in any text editor. These scripts were written in bash for use in a UNIX environment. They require they require additional scripts from scripts from Baute et al. (2016), and the programs Trimmomatic (version 0.36; Bolger et al., 2014), BWA-MEM (version 0.7.15; Li & Durbin, 2009), Picard (version 2.23.8; Broad Institute https://broadinstitute.github.io/picard/), SAMtools (version 1.3.2; Li et al., 2009), GATK (version 3.8; McKenna et al., 2010), VCFtools (version 1.16; Danecek et al., 2011), and Plink (version 1.9; Chang et al., 2015).
The files containing scripts used for analyses were written in and require R (version 3.6.3; R Core Team), and the R package pcaMethods (version 1.78.0; Stacklies et al., 2007)., # Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows

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This dataset contains all the metadata, barcodes, and photos associated with the samples included in the study \"Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows\" by Mcallum, Askelson, Fogarty, Natola, Nikelski, Huang and Irwin, as well as all scripts used in the bioinformatics pipline (Bash and perl) and data analyses (R).
Associated sequences can be found on the SRA as part of the BioProject \"Genotyping-by-sequencing reads from the bird genera Sphyrapicus, Zonotrichia, and Leiothlypis\"

## Description of the Data and file structure

barcodes_plate1.txt - Contains sample names barcodes for samples included in this study on plate 1 (\"Plate 1 - Zonotrichia, and Leiothlypis GBS Library\" on SRA). This is used by the demultiplex and trim perl script i...