Domestication robbed stallions of genetic variation

Modern stallions almost certainly lost the genetic diversity their ancient ancestors after domestication, a new study has revealed.

In contrast, their wild ancestors – male horses from the Yukon, Siberia and Alaska – were much more genetically diverse. So too were domestic stallions from nearly 3,000 years ago.

This suggests that some level of genetic variation still existed in male horses a couple of thousand years after domestication, and that this must have been lost only recently. Horses are thought to have been tamed around 5,500 years ago.

Dr. Sebastian Lippold from the Max Planck Institute for Evolutionary Anthropology is lead author of the study, published in the journal Nature Communications. He said:

At some point over the last 500 years or so, the domestication process has led stallions to lose their genetic diversity. But female horses are different; they have a much wider range of genes. The big question is: why is there a difference between males and females?

Genetic diversity is important for all living things. Species with a wide range of genes tend to produce offspring with a host of different characteristics. This lets them adapt more easily to different conditions. But creatures with little genetic diversity are prone to turning out young that are genetically alike and so more susceptible to disease.

While this isn’t a problem for modern horses, scientists have until now struggled to explain the difference between stallions and mares.

Low levels of genetic diversity among male domestic animals are fairly common: sheep, cattle and dogs all have very little variation in the genes on the male Y-chromosome. It’s even worse in horses: a recent study which analyzed DNA from 52 modern stallions from 15 different breeds showed that all but one failed to show any diversity in the Y-chromosome. Professor Michael Hofreiter from the University of York, co-author of the study, said:

It could be down to low genetic diversity in wild male horses because of the harem mating system. Or it could have resulted from domesticating just a few or a single stallion, or even extreme breeding practises – using just one stud to mate with lots of different females.

To figure out the most likely explanation, scientists have to analyze DNA from both the paternal and maternal lines.

This is easier said than done: until now, they have tended to focus on DNA from the powerhouses of the cells – the mitochondria – because this DNA tends to survive for longer than DNA from the male line on the Y-chromosome. The only snag is mitochondrial DNA tells scientists only about female ancestry. Another problem is that ancient Y-chromosome DNA breaks up into tiny pieces, which makes working out the original sequence of the DNA challenging.

But rapid advances in DNA sequencing technology have let Lippold and an international team of researchers analyze tiny fragments of ancient Y-chromosome DNA from the remains of wild horses from the Yukon, Siberia and Alaska.

Indeed, this is the first time anyone has successfully sequenced DNA from fragments of ancient Y-chromosome.

The researchers analysed DNA from horses that lived up to 47,000 years ago, as well as from the 2,800-year-old remains of a domesticated horse in Siberia. They then compared these sequences with DNA from modern stallions and Przewalski’s horses from Mongolia. Przewalski’s horses are thought to be the closest living wild relatives of today’s domesticated horses. Hofreiter said:

We expected to find more diversity in ancient horses, but not as much as we found.

As well as finding a great deal of genetic diversity in ancient wild stallions, they found that Przewalski’s horses are more closely related to today’s horses than to the ancient horses they investigated. Lippold said:

The next thing to find out is when exactly did stallions lose this genetic diversity? And what breeding practices led to this loss?

The team’s findings demonstrate that researchers can now use sequencing technology to analyze tiny DNA fragments to find out the evolutionary history of species.