The largest non-human genome project has just been completed and guess which other earthling species they focused on? Horses! My brother is a medical geneticist so he shot me this study the moment it crossed his desk. He titled his email: “Horse genetics – sad”
And yes, unfortunately, I have some rather sad news for those of us who love this species. But there are also some really cool pieces of interesting information that came to light as scientists pulled DNA from Equus bones up to 43,000 years old. So let’s start with the good stuff…
The study, Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series, discovered that mules have been bred since at least 2200 years ago. This is remarkable because it shows that the mule genetic traits of sure-footedness, disease-resistance, and being hard working, were desirable enough to make up for sterility (which made the animal more costly).
And speaking of ancient horses… you may already know that domestic and Przewalski’s horses are the only two surviving horse lineages alive on the planet. However, this equine genome project made a startling discovery when they examined three horse bones from 5,000 – 43,000 years ago. The bones showed “morphological affinities” to another extinct equine breed, known as Equus lenensis. Raise your hand if you’ve never heard of Equus lenensis before!
They then discovered that Equus lenensis made contact with another previously unknown lineage in the Siberian Islands about 33,000 years ago, which resulted in some mingling of genes – but they have no idea what this other lineage is, or where it came from, so they just refer to it in the study as a “ghost lineage”.
Ancient ancestors of modern breeds
DNA shows that certain modern breeds native to Europe (like Friesian, Connemara, Sorraia and Duelmener), belonged to another clade (group that shares a common ancestor) that first showed up in Croatia at the same time the Arab raids on the Mediterranean coasts (including Croatia) were at their peak, around the 9th century. The earliest identification of this particular clade was in two Sassanid Persian horses from Iran. So as the Islamic conquests spread across Europe and Asia, so did the bloodlines of the Arabian horse.
Meanwhile, other horses in northern Europe (Aukštaičiai, Lithuania) did not belong to this clade. Instead, these northern European horses formed a sister clade with Pictish horses from Britain, Viking horses, and one Estonian horse – and these genes show up in the modern Shetland and Icelandic ponies. Icelandic horses are valued for their special tolting gait, which is a more comfortable four-beat gait for riding long distances than either a trot or pace gait. I highly recommend the book, A Good Horse Has No Color: Searching Iceland for the Perfect Horse by Nancy Marie Brown if you want to learn about Iceland or the breed. But getting back to our genome study, here’s another cool piece of data:
“The DMRT3 allele [genetic marker] that causes ambling and improves speed capacity in Icelandic horses was first seen in a Great Mongolian Empire horse (TavanTolgoi_GEP14_730) and slowly gained in frequency thereafter.”
The recent decline of Equus
Now for the sad news… After tens of thousands of years of genetic diversity – remember diversity builds strong, hardy, disease-resistant, intelligent species, communities, ecosystems and planets – the last 200 years of humans breeding horses paints a less rosy picture.
Genetic markers show a 16% reduction in the diversity of horse breeding stock within the last few centuries – which tracks alongside significant changes in agricultural practices of maintaining only a small breeding stock of stallions. This reduction of genetic diversity among breeding stock increases the rates of genetic mutation; which can result in an increase in disease and disability.
In the last 200 years, breeding practices narrowed to focus on very few types of temperament, traits, conformation etc. considered to be ‘desirable’. The modern penchant of breeding for certain ‘desirable’ colors or coat patterns further concentrates these potentially damaging genes. Concurrently, modern breeding practices have greatly reduced the chance of being able to eliminate these “deleterious variants from domestic horse stock” – because they’re now present in most horses.
As the number of stallions has greatly reduced, this has also limited Y chromosome diversity. The Y chromosome is enriched in genes that influence sperm count, number and sperm activity. The rise to dominance of specific stallion lines post-Renaissance is alone responsible for a 10-fold drop in Y chromosome diversity. Certain genetic alleles involved in racing (MSTN and PDK4 and ACN9) rose in frequency in the last 1100 years, showing that breeders increasingly selected for fast horses. In fact, from the Middle Ages onward, Arabian genes were present in most stallions.
I mean, who doesn’t love the speed, intelligence and emotional responsiveness of the Arabian horse? But the way biodiversity works, is that the broader the spectrum of variety, the more resilient is the ecosystem, the forest, the species, the planet. So when you reduce diversity because there is not enough land for a species to naturally migrate, mix genes and breed according to their body wisdom (or evolutionary drive), and the majority of breeding is done by us narrow-minded humans, who just want fast, beautiful, or battle-worthy horses, you get results like this:
“Most strikingly, we found that while past horse breeders maintained diverse genetic resources for millennia after they first domesticated the horse, this diversity dropped by ∼16% within the last 200 years. This illustrates the massive impact of modern breeding and demonstrates that the history of domestic animals cannot be fully understood without harnessing ancient DNA data.”
The study authors suggest that due to this accumulation of undesirable genetic traits in modern horses, future studies should look at whether veterinary medicine is able to limit the impact of these harmful genetic variants.
It’s a grim picture as human expansion shrinks wild land to the point that most of us are trying to reduce horse breeding – so that less horses are sent to slaughter. But this study is also a call to those still involved with breeding, or with conservation, to hold the issue of genetic diversity paramount.
I recently read a memoir by the famous Arabian breeder, Sheila Varian. In the book she talks about how the other breeders in California were doing a lot of line breeding (inbreeding) to produce horse after horse that looked a certain way. They weren’t considering the totality of the horse; quality of temperament, personality, physical skills, health, or capability. They simply wanted to breed/sell horses that looked as cookie-cutter as possible. Sheila was one of the first breeders to import stallions from Poland.
Conserving genetic diversity in equines
At least there are still some pockets like this last remaining feral herd in Germany of the Duelmener horse (Dülmener) The yearling stallions are culled annually (since 1907) and sold to be used as children’s ponies or carriage horses – in this way, they make sure the herd numbers do not exceed the conservation land.
Equine ethologist Lucy Rees has been instrumental in preserving a feral herd of Basque Pottokas in Spain – population excess is also culled so the horses can remain self-sustaining on the available land. And the UK has a few free-roaming feral horse preserves.
Even Russia has realized the vital contribution feral horses make to an ecosystem as 6 Przewalski horses have been released into a reserve in Orenburg:
“The reintroduction program was the brainchild of the Severtsov Institute of Ecology and Evolution at the Russian Academy of Sciences, and the Orenburg Reserve. Its steppe territory is the historic home of the Przewalski horse, and the steppe needs this horse to survive, literally.
“In steppe ecosystems these animals contribute to their recovery,” said Olga Pereladova, the head of the World Wildlife Fund’s Central Asian program. “If horses are not grazing in the steppe it deteriorates because vegetation is not trampled; overabundance of grass can cause fires.”
According to the Severtsov Institute, it is important not only that the horses have adapted to the new conditions of the Ural steppes, but also that they do not mix with farm-raised horses when stallions expel competitors from the group.
Because if that were to occur, the unique gene pool would be lost. So the Przewalski horses have been initially placed in a fenced-off reserve, allowing for enough time to pass until a stable population capable of existing under natural selection can be formed. What might that magic number be? The Institute figures it is “necessary to have 1,000 horses, with half being of reproductive age.”
Oh how wonderful it would be to have 300,000 acres of protected land and put family herds of the most genetically diverse horses left on this planet together, where they can interbreed and create more genetic diversity in Equus caballus. Wouldn’t that be amazing! Ted Turner or John Malone, are you listening…?