Introduction

The history of the dog begins with its domestication during the Mesolithic, its spread and adaptation to diverse human settlements, artificial selection for distinct working roles, and finally the establishment of closed breeding populations conforming to specific phenotypes. Each of these processes has influenced the pattern of genetic variation in modern dog lineages. Since the sequencing of the first dog genome over 10 years ago, diverse collections of genotyped and sequenced dogs have given us an unprecedented glimpse at the demographic and selective forces that have shaped the dog genome.

Village Dogs

The majority of the 700 million dogs alive today, like the earliest domesticated dogs, live their lives as free-breeding human commensals known as "village dogs." The structure of populations in many ways mirrors that of human populations - ubiquitous gene flow creating genetic isolation by distance among populations, with additional evidence for admixture with European dogs in some areas. Whereas human genetic diversity is highest in Africa, village dog diversity is highest in Central and East Asia, suggesting either a domestication origin in this region, or a significant population expansion and spread from Asia that wiped out the genetic legacy of more ancient populations. Population turnover is evident from ancient DNA analysis of pre-Columbian dogs of the New World as well as in pre-Bronze Age European dog populations demonstrating the importance of some human migrations in shaping extant dog populations.

Signatures of selection apparent in village dogs include traits selected during domestication as well as adaptations that appeared subsequently as humans and dogs coevolved through the Neolithic. Approximately half of the regions highly differentiated between dogs and wolves include genes involved in nervous system development that may have been involved in behavioral changes during dog domestication. Other regions are involved in starch and fat metabolism and likely reflect genetic changes occurring as a consequence of the development of agriculture.

Purebred Dogs

The era of modern breeding has brought about a substantial reduction of genetic diversity within certain dog lineages. On average, purebred dogs exhibit 20% autozygosity, although the rate varies substantially within and across breeds. Strong signatures of selection in modern breeds correspond primarily to large-effect quantitative trait loci (QTLs) underlying morphological phenotypes such as body size, skull shape, fur type, and coat color. Although selective sweeps during domestication tended to encompass genes involved in behavior, selective sweep signatures across modern dog breeds do not appear to be driven by selection for behavior, even though behavior can vary substantially across breeds. Like many complex canine diseases, most behavioral traits in dogs are highly multigenic, and the identification of causal loci underlying these traits will require substantial cohorts of densely genotyped or sequenced dogs.