Abstract

Although a large part of the global domestic dog population is free-ranging and free-
breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their
ancestry relations to pure-breed dogs is limited, and indigenous status of FBDs in Asia is
uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show
that they display weak genetic structure, and are genetically distinct from pure-breed
dogs rather than constituting an admixture of breeds. Our results suggest that modern
European breeds originated locally from European FBDs. East Asian and Arctic breeds
show closest affinity to East Asian FBDs, and they both represent earliest-branching
lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of
ancestral distributions indicates a gradual westward expansion of East Asian indigenous
dogs to the Middle East and Europe through Central and West Asia, providing evidence
for a major expansion that shaped the patterns of genetic differentiation in modern
dogs. This expansion was probably secondary and could have led to the replacement of
earlier resident populations in Western Eurasia. This could explain why earlier studies
based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA
and archaeological data point to Western Eurasia.