Paleogenomics -- the prehistory of modern dogs

November 06, 2020

An international team of scientists has used ancient DNA samples to elucidate the population history of dogs. The results show that dogs had already diverged into at least five distinct lineages by about 11,000 years ago and that their early population history only partially reflects that of human groups. Dogs were the first species to be successfully domesticated by humans, and they have been our close companions for at least 15,000 years. In spite of the long and intimate relationship between the two species, little is known about how dog populations diversified and dispersed around the world - or to what extent these developments were linked to human migrations. A large-scale international collaboration now sheds new light on these issues. "With the aid of genetic and statistical analyses, we were able to reconstruct the population history of prehistoric dogs, and investigate its relationship to that of humans," says Laurent Frantz. Frantz (formerly at Queen Mary University of London) was recently appointed Professor of the Paleogenomics of Domesticated Animals at Ludwig-Maximilians-Universitaet (LMU) in Munich and is one of the lead authors of the new study. "Our results revealed that the migration patterns of humans and dogs did not always coincide," he adds.

Frantz and his colleagues sequenced a total of 27 ancient dog genomes from Europe, the Near East and Siberia, the oldest of which dates to 10,900 years ago. Their results demonstrate that dogs had already diversified into distinct populations prior to that time. Five separate lineages can be distinguished in the data: Arctic, American, Near Eastern/African, Asiatic and European. The European lineage, to which the great majority of today's most popular breeds belong, is the result of hybridization between the Arctic and Near Eastern/African lines. "One of the biggest surprises for me was that we detected only a minor amount of gene flow from wolves to dogs," Frantz says. "In contrast to the case with many other domesticated pets, the genetic contribution of the wild ancestors of dogs left very little sign in their genomes following their initial domestication. He speculates that this might reflect strong selection on the part of humans against wolf hybrids - which were perhaps more aggressive.

In order to trace the relationships between the population histories of dogs and humans, the team compared the ancient dog genomes with genetic datasets for humans, obtained from DNA samples that were of comparable age, geographical origin and cultural context to those of the canine samples. This comparison revealed that certain aspects of the population history of the dog could indeed be correlated with that of their human contemporaries. For instance, the first farmers, who migrated to Europe and Africa from the Levant during the Neolithic period, were apparently accompanied by their dogs. These then interbred with dogs domesticated by the hunter-gatherer cultures that they encountered in their new homes. However, the resulting diversification of prehistoric dogs has left hardly any traces in the genomes of their modern European descendants. "A process of homogenization subsequently set in, the causes of which remain unknown. In fact, we found that the genome of a dog found at a 5000-year-old site in Southern Sweden can explain practically all of the genetic heritage of modern European dogs. This means that a single population with ancestry similar to that of this individual replaced all other populations on the continent," Frantz explains.

In other cases, however, the migratory patterns of humans and their hounds do not run in parallel with each other. For instance, the migration of peoples from the Eastern steppe zones during the Bronze Age not only led to a dramatic cultural transition, it also left a clear imprint on the genomes of the European populations of that era - but not on those of their dogs. In other words, the arrival of migrants from the steppes did not lead to large-scale and long-term shifts in the genetic heritage of European dogs. The researchers suspect that factors such as trading patterns, preferences for particular types of dog, variations in susceptibility to infectious diseases, or the adoption of local breeds by the incoming population could account for this striking finding. When, where and how often wolves were domesticated by humans are issues that remain controversial. The fact that dogs had already diversified into several different lineages prior to 11,000 years ago points to a long prehistory during the Paleolithic period. "Our data support the idea that dogs were domesticated only once, and subsequently dispersed across the globe together with humans," says Frantz. In his view, the question of where the initial domestication took place is still an open one, which requires further investigation.

Ludwig-Maximilians-Universität München

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