NEW YORK (GenomeWeb) – Researchers have developed a phylogenetic tree of modern dogs that reflects how different breeds were developed.
Researchers led by the National Human Genome Research Institute's Elaine Ostrander created a database of 161 dog breeds that they then placed into a cladogram based on how closely they are related. As they reported today in Cell Reports, the researchers were able to trace recent admixture between different clades and examine the effects of migration. They also found that some dog traits — such as herding — likely arose more than once.
"First, there was selection for a type, like herders or pointers, and then there was admixture to get certain physical traits," study co-author Heidi Parker from NHGRI said in a statement.
To develop their cladogram, Ostrander and her colleagues used the Illumina CanineHD bead array to genotype samples from 938 dogs volunteered by their owners, representing 127 breeds and nine wild canids. They combined that information with data from 405 additional dogs that had been genotyped using the same chip and whose data was publicly available.
Using both an identity-by-state distance matrix and a neighbor-joining tree algorithm, the researchers developed a bootstrapped cladogram with 23 well-supported clades. They noted that these multi-breed clades reflected common geographic origins, behaviors, or appearances. For instance, the flat-coated, golden, and the Labrador retrievers were grouped together.
By calculating identical-by-descent haplotype sharing, Ostrander and her colleagues investigated hybridization between the clades to find that most dog breeds did not share large haplotypes outside their clade or only shared with one other breed.
However, a small number of breeds exhibited a large degree of haplotype sharing with other clades. This suggested to the researchers that those breeds were either recently created or contributed to the creation of multiple other breeds.
For instance, they noted that pugs were grouped with the European toy breed Brussels griffon, but shared haplotypes with Asian toy breeds as well as with small dog breeds in other clades. This could reflect the pug's exportation from Asia and subsequent contribution to other small breeds, the researchers said.
Some breeds were divided based on collection site, the researchers noted. For instance, US-based Tibetan mastiffs exhibited an importation bottleneck and less diverse gene pool than Tibetan mastiffs in China. Likewise, they found the average inbreeding coefficient of US salukis to be twice as high as other salukis. Additionally, US cane corsos shared haplotypes with Rottweilers that Italian cane corsos did not.
Though dogs have been in the Americas for thousands of years, Ostrander and her colleagues noted that the original New World dogs were thought to have been nearly wholly replaced by European ones. However, based on their positions on the cladogram, the researchers suspect that the Peruvian Hairless dog and the Xoloitzcuintle likely descend in part from those New World dogs.
"What we noticed is that there are groups of American dogs that separated somewhat from the European breeds," Parker said. "We've been looking for some kind of signature of the New World Dog, and these dogs have New World Dogs hidden in their genome."
Some dog traits also cropped up more than once, according to the researchers' analysis. For instance, herding dogs — which often use different approach to control their flocks — arose in different geographic locations. "What that also tells us is that herding dogs were developed not from a singular founder but in several different places and probably different times," Ostrander added.