March 18, 2010

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.


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.



eurologist said...

So, what are they trying to say?

- Documented European dogs from ~30,000 years ago are descendants of middle-Eastern wolves;

- the above dogs were replaced with new ones, descendant from middle-Eastern wolves; or

- almost all dogs, at any time, are descendants of middle-Eastern wolves.

I am a bit at a loss, here...

onur said...

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

So perhaps the old European dogs weren't so much closely associated with humans. But maybe afterwards a new set of dog breeds from the Middle East, which were more closely assoicated with humans, replaced (or almost replaced) all others, including the old European dogs.

onur said...

Addendum: The old European dogs may have been descended from European wolves, while the later Middle Eastern ones, which would replace them (according to my hypothesis), were descended from Middle Eastern wolves. So maybe there were multiple independent dog domestication events in various parts of the world during the Upper Palaeolithic, which would be obscured due to the advancement of the Neolithic colonizers from the Middle East, who carried the newly domesticated more human-friendly Middle Eastern dog breeds with them, eventually leading to the total or almost total replacement of all dog breeds unrelated to the Middle Eastern breeds. I say almost, because the genetic remains of non-Middle Eastern wolves in some still existing dog breeds maybe a remnant (at least partially) of the non-Middle Eastern domestication events I hypothesized.

pconroy said...

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 is exactly the point I have made over a year ago in term of African genetic diversity. Africa is seen as very diverse, due to there being a much older* population present and some admixture with it in Africa. This older population are the Bushmen (aka Khoi-San) and possibly also the Pygmies (aka Mbuti).

* By older I mean, that they diverged from other early modern humans a long time ago - maybe 100k yo - and went down their own evolutionary path, and only with the Bantu expansion, have they admixed with other Africans again.

Daniel said...

The "associated to humans" thing recalls something I once saw in a TV documentation about dogs and wolves.

There they claimed that one remarkable difference between dog and wolf would be, that dogs are able to "understand" human facial expressions from birth. While wolves seem unable to learn them, even if grown up with humans and raised alongside dogs.

Its possible to command dogs what to do, by pure movement of the eyes. A wolf suposedly is unable to learn this.

They explained this with "selection" in breeding.

And claimed, humans selected only those wolves as basic breeding material, that proved to be compatible to humans and intermixed them again and again with dogs that proved to be associated with humans and by this creating an artificial lifeform that exists in a symbiosis with the human race.

In other words, dogs genetic setup is made to be a servant to humans.

Well... on the other hand, have dogs proven to be able to survive without their master-race "human".
See those "Dingos", whos anchestors are dogs who ran with humans once.

Andrew Oh-Willeke said...

Interesting study.

We can date the latest possible domestication of dogs in East Asia by the fact the dogs came with proto-Native Americans to the Americas, and by the approximate date of the arrival of the dingo in Australia deduced from fauna extinctions associated with the Dingo's arrival.

Certainly, the archeological referrants mentioned in the study reaffirms the conclusion that dog domestication is pre-Neolithic. Thus, dogs are the first significant domesticate.

The evidence that precludes multiple domestications isn't as clear as it might be. Indeed, it also seems like the study's authors actually argue for a small East Asian domestication in addition to a major Near Eastern domestication.

onur's point about the possibility of a largely extinct early wave European domestication is a good one.

pconroy said...

Andrew, Onur,

I agree with the European extinction of early lineage dogs - and pointed out this a year or two ago, with that paper on Swedish dogs.

In Scandinavia in general dogs have a distinctive mtDNA, which was believed to be ancestral to that area, until ancient dogs DNA was sequenced from the area, and found to be totally different. So it very likely that either Neolithic or Indo-Europeans brought newer dog breeds which wiped out most of the older ones.

If I had to guess the older European dogs would be hunting dogs, while the newer ones would be herding, guard and fighting dogs.

onur said...

The only satisfactory way to test my hypothesis of a total to near total extinction of ancient non-Middle Eastern wolf-descended dog breeds seems to be the ancient DNA testing of the Upper Palaeolithic dog remains.

eurologist said...

I am always a skeptic when it comes to total replacement theories. In addition to testing on remains, Europe would need to be scrutinized as closely as the African and Chinese villages. As I pointed out a while ago, AFAIK no one has gone into the remote villages of Romania, Slovakia, Russia or even less populated areas of western Europe etc. and tested local breeds similarly to other areas in the world.

As to purpose, I think the first Europeans also benefited from the watchdog and fighting capabilities: when it was not feasible for the entire tribe/family to go hunting, and only the stronger men went out, it would have been up to the women, elderly, injured, and teenagers to defend the children and everyone left behind. Especially in small groups, that is a very difficult 24/7 task. Dogs would have alerted the group of danger for an early warning and would have been able to hold back intruders until the firm got their weapons ready.

I agree of course that retrieval of injured hunted animals is a huge thing, given dog's acute sense of smell. With light spears, it is much easier to injure and weaken an animal than to kill it outright.

matt said...

There was a fascinating documentary on dog evolution after domestication a couple of months back entitled "Horizon: The Secret Life of the Dog" (You Tube 6 parts - 1 hour in total)

Some very interesting stuff, eg

1/ dogs know to gauge human emotions by looking at the right side of our face. Which they dont do with other dogs because dog expressions are symmetrical.
(Very funny experiment showing dog doing this).

2/ British dog owners understood perfectly a tape of Hungarian dogs' repetoire of barks.

3/and in part 4 or 5 a lot about the the Russian experiment trying to domesticate foxes to replicate the historical domestication of wolves to dogs.

Been going on for 50 years (ie 50 generations), selectively breeding foxes for tameness.

They are now dog-like, playing with humans, licking humans. But the process is still incomplete. If their human friend goes away they dont pine.

But also, selecting for tameness (only) has led to a difference in appearance. The original Russian foxes were all grey, but now their descendants have variegated markings (eg white patches, etc) like dogs. This was completely unexpected and nobody has explained why it has happened.