Some scholars argue that humans first domesticated wolves in Europe, while others claim this happened in Central Asia or China.
Researchers led by the University of Oxford in the UK reconstructed the evolutionary history of dogs by first sequencing the genome of a 4,800-year old medium-sized dog from bone excavated at the Neolithic Passage Tomb of Newgrange in Ireland.
The team also obtained mitochondrial DNA from 59 ancient dogs living between 14,000 to 3,000 years ago and then compared them with the genetic signatures of more than 2,500 previously studied modern dogs.
Curiously, this population split seems to have taken place after the earliest archaeological evidence for dogs in Europe.
The new genetic evidence also shows a population turnover in Europe that appears to have mostly replaced the earliest domestic dog population there, which supports the evidence that there was a later arrival of dogs from elsewhere.
A review of the archaeological record shows that early dogs appear in both the East and West more than 12,000 years ago, but in Central Asia no earlier than 8,000 years ago.
At some point after their domestication, the eastern dogs dispersed with migrating humans into Europe where they mixed with and mostly replaced the earliest European dogs.
Most dogs today are a mixture of both Eastern and Western dogs - one reason why previous genetic studies have been difficult to interpret.
"Animal domestication is a rare thing and a lot of evidence is required to overturn the assumption that it happened just once in any species," said Greger Larson, from the Oxford University.
"Maybe the reason there hasn't yet been a consensus about where dogs were domesticated is because everyone has been a little bit right," he said.
"The Newgrange dog bone had the best preserved ancient DNA we have ever encountered, giving us prehistoric genome of rare high quality," said Professor Dan Bradley, from Trinity College Dublin.
The study was published in the journal Science.
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