Geographic Structure of Y-Chromosome, Mitochondrial, and Autosomal Domestic Dog Diversity

Patterns of domestic dog (Canis Lupus familiaris) diversity have been described using uniparentally-inherited markers, but the origin of the domestic dog, the role of post-domestication introgression from wolves in the dog genome, and the level of geographic structure outside East Asia remain unclear.   In previous studies Y-chromosome and mitochondrial (Mt) data have been analyzed separately.   We combine Y-chromosome, Mt, and autosomal data in order to clarify patterns of global diversity in dogs.  Genotyping was performed using a semi-custom HD Illumina array on 4,237 dogs (including 2,184 males).  Representatives of 185 breeds and 332 village dogs from throughout Africa, the Americas, Asia, and the Middle East were genotyped.   The array provides 173,276 autosomal SNPs, 537 mt SNPs, and 208 Y-chromosome SNPs.  The large sample size and the number of markers from across the Y-chromosome and Mt allowed for the discovery of previously undescribed haplotypes.  Although the majority of dogs exhibit previously described common Y and Mt haplotypes, the newly identified haplotypes provide evidence of geographic structure especially in African, Australasian, and American dog populations.  Regionally specific mtDNA clades were identified for all regions except Europe.  The Y-chromosome exhibits less diversity than the Mt and we identified fewer total haplotypes.  However, new unique African, East and West Asian, and Australasian haplotypes were identified.  Autosomal data from a dense SNP panel allows for the fine scale resolution of admixture blocks. Combined analysis of haplotype and admixture data provides a more complete picture of the geographic structure and diversity of dogs throughout the world.