Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

• Main Authors: Shannon, Laura M., Boyko, Ryan H., Castelhano, Marta, Corey, Elizabeth, Hayward, Jessica J., McLean, Corin, White, Michelle E., Abi Said, Mounir, Anita, Baddley A., Bondjengo Ikombe, Nono, Calero, Jorge, Galov, Ana, Hedimbi, Marius, Imam, Bulu, Khalap, Rajashree, Lally, Douglas, Masta, Andrew, Oliveira, Kyle C., Pérez, Lucía, Randall, Julia, Tam, Nguyen Minh, Trujillo-Cornejo, Francisco J., Valeriano, Carlos, Sutter, Nathan B., Todhunter, Rory J., Bustamante, Carlos D., Boyko, Adam R.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2016
• Subjects: village dogs; Canis lupus domesticus; haplotype diversity; Canis lupus; Pacific
• Online Access: https://doi.org/10.5061/dryad.v9t5h

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin. Genotype file for Canine HD semi custom array (bed) ShannonBoyko_All.bed Marker file for Canine HD semi custom array (bim) ShannonBoyko_All.bim Sample file for Canine HD semi custom array (fam) ShannonBoyko_All.nopheno.fam Identification for individuals genotyped on the Canine HD semi custom array ShannonBoyko_All.nopheno.txt Genotype file for merged Illumina and Affymetrix array data (bed) ShannonBoyko_Merged.bed Marker file for merged Illumina and Affymetrix array data (bim) ShannonBoyko_Merged.bim Sample file for merged Illumina and Affymetrix array data (fam) ShannonBoyko_Merged.fam Identification for individuals included in merged Illumina and Affymetrix data ShannonBoyko_Merged.ind Mt Marker locations ShannonBoyko_Mt.map Genotypes for Mt haplotypes ShannonBoyko_MtHaplotypeGenotypes Mt ...