<b>A dopamine receptor variant links domestication to behavioral innovation</b>

<h2 dir="ltr">Description of the data and file structure</h2><h3 dir="ltr">Files and variables</h3><h4 dir="ltr">File: Outgroup.recode.vcf.gz</h4><p dir="ltr"><b>Description:</b> The VCF file encompasses genomic data from 15 outgroup species individuals and the following columns standard to the format.</p><h4 dir="ltr">File: Behavior.recode.vcf.gz</h4><p dir="ltr"><b>Description:</b> This VCF file contains genomic data for 94 White-rumped Munia individuals and follows the standard VCF specification, with all required columns and recommended annotations included:</p><ul><li><code>#CHROM</code>: Chromosome number</li><li><code>POS</code>: Position of the SNP on the chromosome</li><li><code>ID</code>: Identifier of the SNP</li><li><code>REF</code>: Reference base</li><li><code>ALT</code>: Alternate base(s)</li><li><code>QUAL</code>: Quality score of the SNP</li><li><code>FILTER</code>: Filter status</li><li><code>INFO</code>: Additional information (e.g., allele frequency, number of samples)</li><li><code>FORMAT</code>: Data format</li><li>Sample columns: One per individual, containing genotype information</li></ul><h5>Specific Fields in <code>INFO</code></h5><ul><li><code>NS</code>: Number of samples with data</li><li><code>AF</code>: Allele frequency</li><li><code>DP</code>: Total depth of reads</li></ul><h5>Specific Fields in <code>FORMAT</code></h5><ul><li><code>GT</code>: Genotype</li><li><code>AD</code>: Allele depth</li><li><code>DP</code>: Read depth</li><li><code>GQ</code>: Genotype quality</li><li><code>GL</code>: Genotype likelihood</li></ul><h4 dir="ltr">File: Code.txt</h4><p dir="ltr"><b>Description:</b> This file contains all the code used for population genetic analysis and single-nucleus RNA analysis in this study.</p><h4 dir="ltr">File: Dataset_S1_DEGS.xlsx</h4><p dir="ltr"><b>Description:</b> The differentially expressed genes between the whole NCL of wild finches and that of domestic finches, and between the whole NCL of wild finches and that of hybrid finches.</p><h5>Variables</h5><ul><li>Gene: gene ID</li><li>p_val: Unadjusted p-value from the Wilcoxon rank-sum test by Seurat.</li><li>avg_logFC: Average log2 fold change.</li><li>pct.1: Fraction of cells in group 1 that express the gene.</li><li>pct.2: Fraction of cells in group 2 that express the gene.</li><li>p_val_adj: Adjusted p-value after multiple testing correction, usually Bonferroni correction.</li><li>Groups: Comparative groups.</li></ul><h4 dir="ltr">File: Dataset_S2_Fst-XPEHH.xlsx</h4><p dir="ltr"><b>Description:</b> Weighted Fst and XPEHH values at each site in the window from 16,939,696 to 17,127,124 on Chr15.</p><h5>Variables</h5><ul><li>Chromosome: Chromosome where the site is located.</li><li>Position: Genomic position (bp) of the site.</li><li>Weighted_Fst: Weighted fixation index (Fst); measures genetic differentiation between populations.</li><li>XPEHH: Cross-population extended haplotype homozygosity; detects recent positive selection between populations.</li><li>norm_XPEHH: Normalized XPEHH; makes XPEHH values comparable across the genome.</li></ul><h4 dir="ltr">File: aggr_harmony_3group_with_celltype.rds</h4><p dir="ltr"><b>Description:</b> A Seurat or SingleCellExperiment object.

Wild finches include "b0S1Y.rds","b0S13Y.rds", and "b0S17Y.rds"; domestic finches include "b0X19B.rds", "b0X12Y.rds", and "b0X16R.rds"; hybrid finches include "b0Z8R.rd", "b0Z17R.rds", and "b0HG.rds.rds".</p><h4 dir="ltr">File: bird_human_homologs.csv</h4><p dir="ltr"><b>Description:</b> Homologous genes between humans and finches are used to perform intercellular ligand‑receptor interactions.</p><h5>Variables</h5><ul><li>bird_gene: gene ID.</li><li>human_gene: gene name.</li></ul><h4 dir="ltr">File: pasa2.longest.filter.gff</h4><p dir="ltr"><b>Description:</b> Genome annotation file of White-rumped Munia (<i>Lonchura striata swinhoei</i>).</p><h4 dir="ltr">File: genome.fa</h4><p dir="ltr"><b>Description:</b> Genome fa file of White-rumped Munia (<i>Lonchura striata swinhoei</i>)</p><h2 dir="ltr">Code/software</h2><h4 dir="ltr">File: Code.txt</h4><p dir="ltr"><b>Description:</b> This file contains all the code used for population genetic analysis and single-nucleus RNA analysis in this study.</p>