“It’s Complicated”: Untangling the Knots in Dog Domestication

by Sandra Murray

Reprinted from: Essential Elements, ShowSight Magazine

Archeological discoveries combined with those from genomes of dogs and wolves have revealed some intriguing insights into the origins of domestic dogs. But sometimes, just when we think we have most of the answers, new discoveries, new genetic information turns our preconceived ideas upside down!

For example, in January of 2012, the University of Arizona released information on an ancient canid skull unearthed a Siberian cave in the Altai Mountains. The university’s Accelerator Mass Spectrometry Laboratory had carbon dated the skull at 33,000 years old. Through studying the skull’s morphology -- its shape -- a joint American and Russian team of archeologists had determined that this skull was that of a dog, not a wolf. Greg Hodgins, one of the researchers at the Arizona lab, explained, “Essentially, wolves have long, thin snouts, and their teeth are not crowded...domestication results in the shortening of the snout and widening of the jaws and crowding of the teeth.” Hodgins added, “What’s interesting is that it doesn’t appear to be an ancestor of modern dogs.” Not an ancestor of modern dogs?!? One of my assumptions bites the dust!

Actually, this Siberian skull shares an ancient time frame with another dog’s skull from a cave in Belgium. That these two dogs lived at approximately the same time but in widely different locations indicates that modern dogs may be descended from multiple ancestors. Not only that, the domestication of dogs may have occurred repeatedly in various geographic locations. The two skulls’ dates of 33,000 years ago place them in a time frame before the ice sheets of the last ice age reached their greatest expanse, called the Last Glacial Maximum -- or LGM. This LGM encompassed a time frame of 26,000 to 12,000 years ago, and it severely tested the survival of the people and the animals alive during that time. It appears that neither the Belgian nor the Siberian domesticated dog lineages survived the LGM. As Hodgins explains, “In terms of human history, before the last glacial maximum, people were living with wolves or canid species in widely separated geographical areas of Euro-Asia and had been living with them long enough that they (canids) were actually changing evolutionarily. And then climate change happened, human habitation patterns changed, and those relationships with those particular lineages of animals apparently didn’t survive.” Previously, no one had ever even considered that these ancient dogs had not survived the last ice age!

In a recent genetic study (January, 2014) to better understand dog domestication, John Novembre, a professor of genetics at the University of Chicago, also discovered that the closest wolf ancestors of today’s dogs may have gone extinct. Then where did today’s wolves come from and are they the ancestors of modern dogs?!? Let’s look deeper into this study.

Researchers examined the genomes of wolves in three likely locations where dogs might have been domesticated: the Middle East, Asia, and eastern Europe. After comparing the genomes of modern dogs to these modern wolves, the modern dogs were not more closely related to any of the three wolves sampled. Novembre added, “That’s the big surprise of the study.” Indeed it is! -- and it blows apart all of our assumptions on the evolution and domestication of dogs.

Dogs and people have been found buried together as early as 14,000 years ago. Previous genetic studies have pointed to China, the Middle East, and Eastern Europe as the origin for today’s domesticated dogs. Novembre and his team wanted to delve deeper to reach a scientific understanding of this domestication. They used high-quality complete genomes from a wolf in Israel, a wolf in China, and one in Croatia to include all of the possible sites of the original dog domestication. Then they also sequenced the full genome of an Australian dingo and an African Basenji. Neither of these dogs have a territory which overlaps with that of wolves, so researchers believed that they would not see the post-domestication interbreeding that so often confuses the genetic trail of how dogs and wolves split.

These high quality, complete genomes allowed the team to examine genetic variations across the entire gene sequences. Using full genomes was crucial, because previous work had been limited to snippets of DNA that were known to vary among breeds of dogs. That does not give a complete picture, because scientists cannot see variations that existed in wolves but vanished in dogs.

The results of the study surprised all of the researchers. The dog genomes all were more similar to each other than to any of the three wolf genomes. Novembre and his colleagues had to conclude that our modern dogs arose from a now-extinct line of wolves. Novembre elaborated: “One possibility is there may have been other wolf lineages that these dogs diverged from that went extinct. So now when you ask which wolves are dogs most closely related to, it’s none of these three, because these are wolves that diverged in the recent past. It’s something more ancient that isn’t well represented by today’s wolves.”

Accounting for gene flow between dogs and wolves due to interbreeding was a key step in the analyses. According to Adam Freedman, a postdoctoral fellow at UCLA and the lead author on the study, this gene flow across canid species was evidently more pervasive than anyone previously knew. As Freedman explained, “If you don’t explicitly consider such exchanges, these admixture events get confounded with shared ancestry. We also found evidence for genetic exchange between wolves and jackals. The picture emerging from these analyses is that these exchanges may play an important role in shaping the diversification of canid species.”

Freedman’s comments make good sense when you consider all the variables that may have gone into the domestication of dogs in that long ago world. We should have realized that such a major development of a new species of canid would never be a nice, straight line that we could easily trace. Instead, one should picture the evolutionary journey of wolf to dog as a heavily branched bush with many of those branches representing genetic exchanges with wolves in various places and times. We also need to see that many of those branches went extinct due to extreme environmental conditions, creating bottlenecks at which only a few lines survived to continue evolving. In fact, by analyzing genome-wide patterns of genetic variations, Freedman and his colleagues discovered that dogs suffered a 16-fold reduction in their population size as they diverged from wolves. The wolves themselves suffered a sharp drop in numbers soon after their divergence from dogs. Novembre speculates that this drop could have resulted from competition for large prey from humans. This crash in both dog and wolf populations implies that diversity among both animals’ common ancestors was larger than what is represented in modern wolves.

In looking at the comparisons between the dog and wolf genomes along with the bottleneck that both species experienced in their populations, the team suggests a time frame for domestication of modern dogs at between 11,000 and 16,000 years ago before the rise of agriculture. The fossil record concurs with this estimation. Those two dog skulls discovered that date at 33,000 years ago were just a blip on the radar that vanished during the last glacial maximum period.

Researchers also found differences in the amount of amylase (AMY2B) genes among different breeds of dogs and also in wolves. Amylase genes help digest starch, and some recent studies have indicated that this gene was critical in dog domestication. For early dogs living in or near human settlements, having amylase genes allowed them to scavenge food containing starchy grains from agricultural societies. When the research team examined genetic data from twelve additional dog breeds, they found that many did, indeed, have high numbers of amylase genes. But those breeds not developed in agrarian societies, such as the Siberian Husky, the Malamute, and the dingo, had only a few of those genes. In addition, they found evidence of amylase genes in wolves, meaning that amylase genes did not develop exclusively in dogs after the two species diverged. The number of amylase genes in dogs may have expanded more recently after domestication.

Given what these latest studies have revealed, we now have a totally different view of wolves and dogs. In actuality, they resemble groups of siblings rather more than ancestors and descendants. For both groups, their original namesakes died off during the last glacial maximum. Complete genomes of modern wolves and dogs cannot reveal either the founding animals of modern wolves or the original progenitors of modern domesticated dogs. John Novembre believes that ancient DNA analyses will be necessary, but so far, the DNA sequences extracted from fossils are incomplete. But just as researchers have recently sequenced the complete genome of the Neanderthal man, so other researchers are zeroing in on sequencing the full genome from fossil wolves and dogs. Novembre said that, “Several groups are hammering away” at the problem and that a full ancient dog genome could be just months away -- perhaps as few as nine.

Stay tuned

Until next time,
Sandra