Dogs were probably domesticated in the Near East rather than East Asia

Nicholas Wade writes in the NY Times:

Borrowing methods developed to probe the genetics of human disease, researchers have concluded that dogs were probably first domesticated from wolves somewhere in the Middle East, in contrast to an earlier survey suggesting dogs originated in East Asia.

This finding puts the first known domestication — that of dogs — in the same place as the domestication of plants and other animals, and strengthens the link between the first animal to enter human society and the subsequent invention of agriculture about 10,000 years ago.

From a methodological standpoint, this study shows how we shouldn't infer population history and dispersals from the study of uniparental markers. It is quite possible that the most recent common ancestor (MRCA) at a locus may have lived at a different location than the ancestral population, prior to its dispersal.

With dogs, mtDNA seemingly coalesces to an East Asian ancestor, a finding that has recently been both challenged and re-affirmed. However, this new Nature paper shows that in terms of overall genomic diversity the Middle East rather than East Asia is the region where grey wolves were first domesticated, becoming the earliest dog populations.

Any locus (in this case mtDNA) may have its MRCA in a location somewhere across its geographical range. In fact it is expected that due to either luck or advantage, successful mutations at every locus may arise throughout a species' range, and indeed should be more likely to arise in more populous areas (more bodies = more new mutations).

It is by looking at multiple genetic loci that the true history of a species may be inferred. But this, too, requires caution, as great genetic diversity may arise from either great antiquity or substantial admixture (being at the crossroads).

Indeed, "central" regions of a species have the tendency to accumulate a greater level of variation, since genetic mutations must travel a shorter distance to get there, from their point of origin.

All in all, I am a priori skeptical of attempts to reconstruct population history (in either dogs or humans) from modern population data. Nonetheless, this study casts serious doubt on the East Asian origin of dogs, and adds support for the Near Eastern hypothesis.

From the press release:

"That research made extrapolations about how the domestic dog has evolved from examination of one region in the mitochondrial genome," Wayne said. "This new Nature paper is a much more comprehensive analysis because we have analyzed 48,000 markers distributed throughout the nuclear genome to try to conclude where the most likely ancestral population is.

"What we found is much more consistent with the archaeological record," he said. "We found strong kinship to Middle Eastern gray wolves and, to some extent, European gray wolves — but much less so to any wolves from East Asia. Our findings strongly contradict the conclusions based on earlier mitochondrial DNA sequence data."

Eighty percent of dog breeds are modern breeds that evolved in the last few hundred years, Wayne said. But some dog breeds have ancient histories that go back thousands of years.

"We sampled both groups, the modern explosion of dog breeds and some of the ancient lineages," he said. "Our data were aimed at resolving questions about the origin of domestic dogs, the evolution of dog breeds, and the history of dog breeds and relationships to their closest wild progenitor, the gray wolf."

The first dogs that appeared in the Middle Eastern archaeological record date back some 12,000 to 13,000 years, Wayne said. Wolves have been in the Old World for hundreds of thousands of years. The oldest dogs from the archaeological record come from Europe and Western Russia. A dog from Belgium dates back 31,000 years, and a group of dogs from Western Russia is approximately 15,000 years old, Wayne said.

"We know that dogs from the Middle East were closely associated with humans because they were found in ancient human burial sites," Wayne said. "In one case, a puppy is curled up in the arms of a buried human."

Some very old strains of dogs, with a history dating back more than several thousand years, may be mixed with modern breeds, enhancing their diversity in certain areas such as East Asia, Wayne said, interpreting the higher mitochondrial DNA diversity in that area of the globe.

There is one small set of East Asian breeds that does not indicate a strong Middle East origin, showing instead a high level of genetic sharing with Chinese wolves. This finding suggests there was some intermixing between East Asian dog breeds and East Asian wolves; the data do not make clear how long ago this occurred.

"However, the vast majority of dogs that we studied show significant levels of sharing with Middle Eastern wolves," said Novembre, a population geneticist who studies genetic diversity and the lessons that can be learned from it.

Nature doi:10.1038/nature08837

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Bridgett M. vonHoldt et al.

Abstract

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1, 2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

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