Inbreeding to create purebred dogs has a deservedly bad reputation, as many of these breeds suffer from genetic diseases. But it turns out that it's not the only culprit. A paper in yesterday’s PNAS delves into the differences between wolf and dog genomes to find out exactly how human influence has increased the risk of dangerous mutation in dogs.

When dogs were first domesticated, they underwent what’s known as a population bottleneck. That is, only a small number of ancestral grey wolves formed the starter population for what eventually became dogs. This starter population had only a smidgen of the overall genetic diversity of wolves, and that’s all the genetic diversity that dogs started out with. Then, more recently, humans caused more bottlenecks when they started to selectively breed dogs. This narrows down the pool of genetic diversity even further.

To find out how these bottlenecks have affected dogs, the researchers sequenced the genomes of 46 dogs from 34 different breeds, as well as from 25 “village dogs,” the free-breeding dogs living in human settlements worldwide. They compared this to the genomes of 19 wolves.

Cousin Dad

Dogs, like the vast majority of animals, have two sets of chromosomes: one from the father and one from the mother. The two sets are different from each other in some places, reflecting the genetic differences of the parents.

This means that the similarity between the two sets of chromosomes can give clues about a group's genetic diversity. Seeing how often the two sets match up with one another, and how often they differ, can provide data on how closely related an individual’s ancestors were to one another. If the two sets are very similar, it increases the risk of harmful mutations appearing in both sets.

As expected, breed dogs have much more similarity between chromosome sets than wolves do. We know that breed dogs are inbred, so this isn’t a huge surprise, although it does help to specify exactly how much the inbreeding affects their genomes. Village dogs were also affected, though. They sat somewhere in between wolves and breed dogs, probably reflecting the initial population bottleneck caused by domestication.

Cooking up proteins

A loss of genetic diversity is a problem because it increases the risk of harmful mutations. But not all mutations are harmful—most don’t really do much at all but can still provide important data on the genetic history of a species.

DNA acts as a recipe for the amino acids that make up proteins, which in turn govern the biological functions of the organism. In many cases, a small tweak to the recipe (the DNA sequence) still results in the same amino acid. That means that there are genetic sequences that can mutate a little bit without having any effect on the resulting protein. Because these mutations don’t harm or benefit the organism, they aren’t acted on by natural selection.

On the other hand, there are some amino acids that are only encoded by a very specific DNA sequence. If a mutation happens on that DNA sequence, a different amino acid appears in the protein—the recipe is changed. That results in a different protein, which could result in an important change in the organism. If the change is beneficial, it spreads throughout the population through natural selection; typically, however it’s harmful and is selected against.

In any animal’s genome, there will be some of both kinds of mutation: the recipe-tweaking kind that keeps amino acids the same, and the recipe-overhauling kind that changes amino acids. Since the latter usually results in changes that can be selected against, these mutations are likely to disappear. This means there should be fewer recipe-overhauling mutations compared to recipe-tweaking ones.

If there’s a higher rate of recipe-overhauling mutations, it’s a sign that they’re accumulating over time. This means natural selection isn’t getting the chance to weed out the harmful mutations.

When the researchers compared this rate in dog and wolf genomes, they found that it was higher in dogs than in wolves. It wasn’t limited to just a few breeds, either: it applied across the board. This suggests that the bottlenecks brought about by domestication have made it less likely that harmful mutations have been removed by natural selection.

Genetic illness

So what’s the actual effect of these mutations? To figure this out, the researchers looked at genetic sequences that are common across multiple species. This is a sign that these sequences are important, meaning that any mutation on them is likely to be harmful.

They found that dogs had around 2.6 percent more of these mutations than wolves did, a small but statistically significant increase. It’s a problem likely to be compounded by inbreeding, because dogs could end up with two copies of a harmful mutation. That said, the rates aren’t astronomical. The authors write that they're roughly comparable to natural demographic processes (like migration).

Inbreeding isn’t the only danger—the artificial selection imposed by humans can increase the risk of genetic disease. When dog breeders select a certain characteristic, like hair color, they’re really selecting a DNA sequence that gets passed down through generations. At the same time, they’re also unwittingly selecting for nearby bits of DNA, which hitchhike along with the selected sequence. If harmful mutations occur in this hitchhiking DNA, the mutations can end up actually being selected for and propagated by dog breeding.

The researchers found evidence of this by looking at sequences of DNA that are associated with selection during breeding. They found more harmful mutations in these sequences than would be expected by just chance. “Our results raise ethical concerns about the creation of fancy breeds,” the authors write. For example, they say, selecting for black coats in poodles seems to also increase the chance of cancer of the nail beds.

These results give us a better understanding of the genomes of our closest companions, but they have a wider reach, too. For a start, humans have also undergone population bottlenecks, so figuring out how this has affected dog genomes can help us understand our own.

There are also many, many other species facing severe bottlenecks: all the ones we’re pushing out of their habitats and otherwise killing in large numbers. Efforts to maintain small populations of endangered species often emphasize avoiding inbreeding, but this research points out that there are other processes at play. Most importantly, just maintaining population size to keep the bottleneck as wide as possible is an important contributor to genetic health.

PNAS, 2015. DOI: 10.1073/pnas.1512501113 (About DOIs).