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: Dataset
• Language: unknown
• Published: 2016
• Subjects: village dogs; Canis lupus domesticus; haplotype diversity; Canis lupus; Pacific
• Online Access: https://zenodo.org/record/5010600; 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.bedMarker file for Canine HD semi custom array (bim)ShannonBoyko_All.bimSample file for Canine HD semi custom array (fam)ShannonBoyko_All.nopheno.famIdentification for individuals genotyped on the Canine HD semi custom arrayShannonBoyko_All.nopheno.txtGenotype file for merged Illumina and Affymetrix array data (bed)ShannonBoyko_Merged.bedMarker file for merged Illumina and Affymetrix array data (bim)ShannonBoyko_Merged.bimSample file for merged Illumina and Affymetrix array data (fam)ShannonBoyko_Merged.famIdentification for individuals included in merged Illumina and Affymetrix dataShannonBoyko_Merged.indMt Marker locationsShannonBoyko_Mt.mapGenotypes for Mt haplotypesShannonBoyko_MtHaplotypeGenotypesMt haplotype calls for ...