2026-10-14T21:33:02Z
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oai:figshare.com:article/33948616
2026-09-21T05:29:50Z
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<b>A dopamine receptor variant links domestication to behavioral innovation</b>
Ying Xiong (25077460)
MW D (17596869)
Ziyi Wang (25077621)
Qi Yang (25077623)
Lirong Zuo (21022701)
Limin Wang (18252532)
Liqing Fan (5684831)
Yalin Cheng (9340337)
Kai Song (25077642)
Dongming Li (21022722)
Fumin Lei (9340552)
Biological adaptation
Genomics
Animal behaviour
Genomics and transcriptomics
Domestication Syndrome Hypothesis
behavioral innovation
Social selection theory
<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>
2026-09-21T05:29:50Z
Dataset
Dataset
10.6084/m9.figshare.33948616.v1
https://figshare.com/articles/dataset/_b_A_dopamine_receptor_variant_links_domestication_to_behavioral_innovation_b_/33948616
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