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Decoding the Dog Genome

A notable change in the dog from the wolf is that females enter first estrus at six months to one year of age. Breeders in the rural South have long bred their dogs at first heat, and it may well be a custom dating back centuries. Australian dingoes, living in packs independent of men, start breeding around two years of age, according to dingo expert Laurie Corbett in The Dingo in Australia and Asia. Beyond that, my searches fail to pull down any calculation for the generation time for dogs. Clearly, that needs more examination.

In a commentary accompanying Nature’s presentation of the genome, Hans Ellegren, an evolutionary biologist at Uppsala University, raised another qualifier, saying that if “repeated back-crossing has occurred” between dogs and wolves, Lindblad-Toh’s model of the dog’s origins “would have to be revised.”

The Broad Institute team’s analysis appears on firmer footing when it comes to placing breed formation within the past 200 to 300 years. Breeds are formed through consolidation of working dogs of an existing type into a more consistent form, through hybridization and inbreeding to reconstruct a breed, and through building on a small number of imported animals. Early dogs bred rather freely, and—because in sexual reproduction, the chromosomes from the sire and the dam are recombined to form the single chromosome passed on from each and because alignments are not perfect—haplotypes were broken up, becoming shorter and more scattered over the generations of random breeding.

Through inbreeding from a small gene pool to create their particular breed, humans unknowingly selected a small group of overlapping chromosomes carrying the genes for the traits they wanted—and for some diseases they didn’t want. From that came the breed’s distinctive pattern of large homogeneous haplotype blocks and shorter heterogeneous ones, which selective breeding has sustained.

A notable exception to this model appears to be the Labrador Retriever, which replaced the “old yellow dog,” or cur dog, as America’s most abundant big dog and so is less inbred than other breeds, except in some lines. The English Springer Spaniel and Golden Retriever are more inbred than Labs but less than most other breeds. But all three show the pronounced influence of “favorite sires,” whose overuse also serves to limit diversity. In an interview, Elaine Ostrander said research in her lab has indicated a clear genetic break between show Labs and field-trial Labs, and between show and hunting Beagles.

Breeds that passed through a formation bottleneck typically have four of around 10 possible haplotypes, the researchers said. Although the haplotypes and their proportions vary from breed to breed, haplotypes are also shared between them. As the Akita indicates, this arrangement might not extend beyond breeds of western dogs. But it means that researchers can use 10,000 SNPs, a relatively small number, to scan the genomes of dogs within the breed and compare them with those of other dogs in the same breed in order to find genes.

“We now have a whole new tool kit for looking at the evolutionary history of canines and the origins of dogs, where they originated and how they spread, and how often they interbred with local wolf populations,” said Robert K. Wayne, an evolutionary biologist at the University of California, Los Angeles. A 60,000-SNP GeneChip (similar to a computer chip but incorporating DNA) soon to be available from Affymetrix should speed the search for genes that regulate a dog’s phenotype, he added.

Wayne and his lab contributed a new family tree, or phylogeny, of 34 canid species for the Nature paper, showing the time of their emergence during the past 40 million years and solidifying the already strong argument that the wolf is the dog’s nearest relative, while the wolf’s wild kin are, in order, the coyote, golden jackal, Ethiopian wolf, dhole and African wild dog.

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