Embarking on Dog Ancestry Research!

March 1, 2018

Hi Embarkers! Aaron Sams, Research Scientist at Embark, here.

If you are an Embarker that has opted to participate in scientific research, you’re officially a citizen scientist! On behalf of Embark, I want to say thanks for your contribution.

This week, Embark is presenting some of the first research to come out of the data that you and others have given us. We are at the 9th Annual International Conference on Canine and Feline Genetics and Genomics in St. Paul, MN, presenting new results on genetic variation in the dog Y chromosome. Later this summer, we will also be presenting at the 2017 Annual Meeting of the Society for Molecular Biology and Evolution.

While we are also busy researching several important health conditions, this initial research involves understanding the history of dogs. My post below goes through the nitty gritty details. For those readers not interested in the specifics, the short version is that we’ve found some new, strong evidence that the ancestors of dogs in both the Arctic and Africa bred fairly frequently with wild canids, like wolves. This is similar to how people in Europe show evidence of having interbred with Neanderthals. Overall, this information helps us understand the journey of dogs.

We’re making this presentation available here to all of the Embarkers out there that are making this research possible.

Genetic variation in the dog Y chromosome

In dogs, like humans and other mammals, the Y chromosome (from here on, just Y) is one of two sex chromosomes (X and Y). It is found in only males and only in a single copy. This is in contrast to the X chromosome (which is in both males and females) and the 38 other (“autosomal”) chromosomes found in two copies in each cell, one from each parent.

The Y is transmitted from generation to generation from father to son. Because the majority of the Y does not get shuffled through the process of genetic recombination, we can easily resolve the haplotype (the set of genetic variants that are inherited together from one parent on a single copy of a chromosome) carried by each male dog. Dogs carrying the exact same Y haplotype are likely to share a paternal ancestor more recently in time than dogs carrying different Y haplotypes. Mutations arise on Y each generation, therefore haplotypes that derive from distant male ancestors are slightly different. As a result, we can organize these into sets of haplogroups, or closely related haplotypes.

This presentation describes how the Embark genotyping array is allowing us to better resolve genetic variation in the canine Y. It also highlights some of the initial insights that we are gathering into the paternal history of domestic dogs.

Figures

Figure 1.

In the figure above (Figure 1), we illustrate the relationships among unique Y haplotypes that we have observed in Embark customer dogs. In a few cases, this is providing some potentially interesting insights into dog ancestry. For example, we have observed a Y haplotype, H9, that is found in Basenjis and another haplogroup, B1, found primarily in arctic breeds. They are both quite distantly related to other haplotypes in other breeds. This pattern of ancestry may suggest that these haplotypes were introduced from wild canid populations (introgressed) into the domestic dog population fairly distantly in the past. These patterns will help us understand the history of interbreeding between wild canids and domestic dogs.

Figure 2 (left) and Figure 3 (right).
In Figure 2 and Figure 3, we have illustrated a few specific cases. In these cases we have been able to split up a previously reported Y haplotype into several new haplotypes. Being able to more finely resolve Y haplotypes in this way is great because it will allow us to understand more fine-scale patterns in the ancestry of dog paternal ancestry.

Figure 4.
Similarly, Figure 4 shows that Embark’s increased Y resolution leads to two things. 1) Observations of a larger number of unique haplotypes overall. 2) A larger number of more rare Y haplotypes.

The future

This is just the tip of the iceberg. As we incorporate more and more data from Embark customers, we will continually seek to better understand the history of humans’ best friend. Understanding variation in Y haplotypes across large, geographically diverse samples of dogs will allow us to address several fun scientific questions. For example: How many males generally contributed to the initial stock of modern dog breeds? Where and when did the Y ancestor of all domesticated dogs live? The evolution of domestic dogs is so closely tied to the human story. Therefore, the answers to these questions can even provide important insights into our own history!

By the way, we can always use more hands (and paws) on deck to answer these questions! To that end, Embark is looking for a highly motivated research scientist and postdoctoral researcher to join our team.

To view the full presentation poster, click here.

Thanks for Embarking with us!