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Decoding the Dog Genome

Comparing the Boxer to the other breeds and the five wild canids, the researchers found that while the SNP rate between different Boxers was 1 for every 1,600 base pairs, it was around 1 for every 900 base pairs between the Boxer and every other breed but the Malamute, which was 1 for every 787 base pairs. According to the breed identification system developed by Elaine Ostrander and Leonid Kruglyak of the Fred Hutchinson Cancer Research Center in Seattle, the Malamute belongs to a class of “ancient dogs” and thus would be expected to be more distant from the modern Boxer than other modern breeds—the shorter the distance between SNPs, the more distant the relationship. The other dogs represented breeds created or consolidated within the past 300 years, like the Boxer. Compared with the Boxer, the wolves had ratios of around 1 SNP for every 580 base pairs, and the more distantly related coyote stood at 1 for every 420 base pairs.

The Boxer’s genome represents “a mosaic of long, alternating regions of near-total homozygosity and high heterozygosity,” the researchers reported in Nature. The homozygous regions, wherein both chromosomes in a pair have identical haplotypes, cover 62 percent of the genome; the heterozygous regions, in which the haplotypes are not identical due to SNPs or genetic variations, 38 percent.

The researchers then scanned the genomes of 20 dogs from each of 10 other breeds, and one dog from each of 24 breeds, ranging from the ubiquitous Labrador and Golden Retrievers to the rare Glen of Imaal Terrier, but always limiting themselves to purebred dogs registered by the American Kennel Club. The analysis by Lindblad-Toh’s team reported in Nature that most dog breeds were similar to the Boxer in terms of number of SNPs, and the relative proportions of heterozygosity and homozygosity were also similar.

The one aberration was the Akita, a Japanese breed created, by Lindblad-Toh’s estimate, some 10,000 years ago for hunting, which passed through a bottleneck in the 1940s in America. The first official Akita in America was a gift from Japan to Helen Keller in 1937.

Using mathematical models that postulated an effective population of 13,000 dogs with an inbreeding coefficient of .12—meaning basically that they are cousins—the researchers concluded that in achieving its current blend of sameness and difference, the dog passed through a major genetic bottleneck 9,000 generations ago, and another 30 to 90 (sometimes given as 50 to 100) generations ago. Assuming a generation time of three years for dogs, they pegged the origin of the dog at 27,000 years ago from perhaps as few as two wolves. Lindblad-Toh said in an e-mail that the founding population of wolves might have been larger—and some geneticists say there must have been several hundred animals involved—but the genome does not appear to record any contribution from them. She also said that there may have been multiple domestication events and back-crosses with wolves at various times and places, as other genetic studies have shown.

I am a fan of ancient dates when it comes to dog origins, and the older the better, but this new offering—a sort of compromise between 15,000 years ago in East Asia, proposed by Peter Savolainen of the Royal Institute of Biotechnology in Stockholm and his colleagues in 2002, and 40,000 to 135,000 years ago that Robert K. Wayne and his lab team at the University of California, Los Angeles (including Savolainen), proposed in 1997.

Geneticists are divided, but archaeologists are not. Darcy Franklin Morey, an archaeologist at the University of Kansas specializing in the dog, says that 27,000 years ago, like the older dates, fails to coincide with the archaeological record, which dates to around 12,000 to 14,000 years. Morey has a paper forthcoming in the Journal of Archaeological Science arguing that the proliferation of dog burials at the time marks the origin of the dog. He does have a point in that as a cultural construct, the dog has left natural history and entered human history. Arguably, then, the molecular clocks used to calibrate its age should be set to human, as well as geologic time. Beyond that, the choice of three years as the generation time for dogs is unexplained and possibly long.

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