Ancestry & DNA: decipher the biology behind your dog’s family tree

Cover Image for Ancestry & DNA: decipher the biology behind your dog’s family tree
John Lindo, PhD
by John Lindo, PhD

A (very) brief history of evolution theory 

Appearances can be deceptive, especially when it comes to understanding how different species relate to each other from an evolutionary perspective. Aristotle fell into this trap when developing his system for classifying organisms into groups via some observable commonality. Some two thousand years later, Charles Darwin did, too, extrapolating even further and proposing that all organisms on the planet, both extinct and extant, stem from a single ancestor. 

Ultimately, these two concepts gave rise to the Tree of Life: a depiction of the relationships between species, all coming from a common ancestor. Trees like these are called “phylogenies,” and for the past 200 hundred years, they have served as one of the foundations of evolutionary theory.

A phylogenetic tree with a Common ancestor (text) of Mammals (text) and on the branches illustrations of Whale, Giraffe, Cheetah, Dog and Wolf, Bear and Seal. Caption left of Dog and Wolf: "Grouped species are closer than species on different branches" and left of the bear and Seal "Seemingly disparate species are sometimes found to be closely related"
The Tree of Life: a depiction of the relationship between species and their common ancestor

Knots on the Tree of Life

Despite the popularity of phylogenies, scientists often disagreed about their construction. How should taxa be arranged? Which common features should hold prominence for classification? 

In addition, we now know that features that seem similar between species do not necessarily mean there is a recent common ancestor. Instead, in some cases, similar evolutionary pressures can lead to a common adaptive solution, a process known as convergent evolution. As a result, using a common attribute like flight to classify species created erroneous groupings between species with vastly different evolutionary histories, such as bats and condors. While this particular example might be obvious, others are not and led to false assumptions and, therefore, misleading phylogenies. 

Enter the genome 

Even before the era of genomics, when now the entire genome of a species can be sequenced in a day, scientists began to suspect that genetic relationships could yield a better understanding of how species and populations within species relate to each other. 

At first, the idea was relatively simple: The more areas of the genome that are shared between species, the closer their relationship. However, when the first evolutionary trees were constructed in this way, relationships that had been “solved” for decades began to fall apart. Even large phylogenies, like those exploring the complex relationships between extant birds, began to be redefined in ways that had not been previously suspected. Seemingly disparate species (flamingos and pigeons) were found to be closely related, while other seemingly similar species (eagles and falcons) were determined to be more distant. 

But why are genomic-derived phylogenies so different from those built with shared physical traits? 

The answer lies in a rather elegant feature of evolution. In organisms that reproduce sexually, the genetic material of the parents shuffles between copies of their genomes before being passed down to their progeny. This ensures that genetic material is transferred from not only the parents, but also from all four grandparents, creating a genome that is actually a mosaic of the organism’s ancestors, going back thousands of years. This vast array of events and relationships is difficult to conceptualize in a hierarchical tree. 

Humans are an example of networked evolution

One of the best examples of how genomics has transformed traditional phylogenies involves our own branch of human evolution. Since Neanderthals were discovered in the 1800s, naturalists thought of them as a distinct species to humans, although closely related given the anatomical similarities between our skeletons. However, the publishing of the Neanderthal Genome in 2010 yielded some unexpected results: Humans and Neanderthals share long stretches of DNA, suggesting gene flow between the two species while they both co-existed in Eurasia, over 30,000 years ago. 

Findings like these add complexity to the ideas behind traditional phylogenies. Instead of thinking of a single common ancestor giving way to an array of species, it’s more informative to consider the vast network of genetic interactions through time that contributed to the genome of each species we see today. 

Creating evolutionary trees for dogs

So how does this all relate to the evolution of the domesticated canine? Can we construct a meaningful evolutionary tree using genomes? 

The answer is yes, but we have to be mindful of how we interpret the exposed relationships. For instance, using genome-level data enables us to catch “hidden” ancestral affinities between populations, arbitrarily defined as a set of interbreeding individuals. But in the world of dogs, where “breed” is often used as a proxy for “population,” there is even greater complexity, given the added layer of subjectivity in how breeds are defined and their reliance on common physical attributes, which, as explained above, does not coincide well with relationships revealed by the genome. 

Recent crosses between two established breeds can further complicate evolutionary relationships by creating new branches on the tree. And keep in mind that evolutionary trees do not need to be static. Trees can take on a more networked approach where gene flow between branches can not only help place a mixed-breed individual but also reveal hidden information about the recent history of that particular dog. 

Your dog’s ancestry

Understanding how canine phylogenies are created can help you interpret the ancestry information you receive from your dog’s DNA test. But even then, the results can be surprising, especially if you’re not expecting a particular outcome (e.g., the report for your purebred dog shows an ancestral composition of more than one breed). 

This brings us back to the conundrum of observable characteristics not matching up with the ancestral information locked in the genome. Remember: The genome is a vast space, holding not only information for observable characteristics but also the events between a network of ancestors that eventually led to your dog. In fact, some of these events go far back into your dog’s evolutionary history to a time when its ancestors were gray wolves, some 30,000 years ago. 

Typically, though, we don’t have to go back far to understand genetic testing results. 

In the case of a German Shepherd

Imagine that you’re the proud owner of a purebred German Shepherd. Then, you learn  that 5% of your dog’s DNA is reported as Xoloitzcuintli, otherwise known as the Mexican Hairless Dog. Your first reaction may be anger or perhaps disbelief. But what is the report actually telling you?

First, it’s important to note that the method employed by Loyal’s genetic testing involves comparing long stretches of your dog’s DNA to a reference panel composed of various dog breeds and wolves. Therefore, the report is not actually telling you that your dog is 5% Xoloitzcuintli. What the test has actually detected is a stretch of DNA that is shared between your dog and the reference panel, in this case the Mexican Hairless Dog. 

The changing ancestral landscape of the Xolo genome and why a German Shepherd may share DNA with the Xoloitzcuintli due to gene flow in the 1900s from the German Shepherd  to the Xolo

But why would an ancient dog from the Americas share DNA with a modern dog breed from Europe? 

Well, the answer goes back to the ancestral complexity locked within the dog’s genome. The DNA test has actually detected a gene flow event between populations, and in this case, it’s not an ancient event but a historical one. The arrival of Europeans had devastating consequences for the human Indigenous populations of the Americas. Unfortunately, these consequences also extended to the indigenous canines. Most canine populations from the Americas are now extinct, while others were systematically crossed with European breeds for different, often nefarious reasons. For example, in Mesoamerica, the Spanish colonizers attempted to exterminate or interbreed indigenous dogs that were culturally important to the Indigenous people. The Xolo was spared complete annihilation due to the efforts of locals in what is now Western Mexico, where the dog was hidden from the Spanish and continued to be bred in secrecy. Decades after the formation of the Mexican state, the Xolo was formally bred and eventually accepted into the AKC. However, recent analyses of the modern Xolo genome have shown stretches of DNA shared with the German Shepherd, perhaps capturing a historical admixture event. 

Putting all of this information together, the results of the DNA test do not suggest that this German Shepherd was improperly bred. Instead, the test is picking up a historical interbreeding event that has led to two seemingly disparate dog populations sharing stretches of DNA.

The canine genomic mosaic: your dog shares DNA with diverse ancestors that are reflected in the make-up of their DNA

Understanding Your Dog’s Evolutionary Journey

As you can see, your canine companion’s genome is a complex place. Locked within this complexity is a remarkable mosaic of evolutionary events that reflect your dog’s ancient and recent ancestry. Genetic breed testing should be taken as a step in understanding that journey. It is a powerful tool that, combined with our other research, helps drive Loyal’s efforts to help all dogs live longer, healthier lives.


  1. Jarvis et al, (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346 (6215), 1320-1331.
  2. Franklin, J. (1986). Aristotle on Species Variation. Philosophy, 61(236), 245-252. doi:10.1017/S0031819100021094
  3. Green et al. (2010) A Draft Sequence of the Neandertal Genome. Science 328 (5979), 710-722.
  4. Valadez, R. (1995) El perro Mexicano. Mexico: Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México. 
  5. Parker, H. (2017) Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development. Cell Reports 19 (4), 697-708.
Jumbo, miniature american shepherd whispers in human's ear
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