Genomes of modern horses reveal domestication secrets of ancient people
A new study reveals the suite of traits that ancient nomadic peoples selected to develop the type of horse that best fit their purposes
This piece was a Forbes Editor’s Choice.
Horses were probably first domesticated by the Botai culture roughly 5500 years ago, somewhere in the vast Kazakh Steppe that lies at the southern end of the Ural Mountains, that traditional dividing line between Europe and Asia. The Botai peoples were a true “horse culture” — highly dependent upon horses, which allowed them to travel quickly and to conquer vast territories — and in fact, they may have even provided the loanword for “horse” to the local language family.
Nomadic Scythians (probably comprising groups of unrelated peoples that shared similar lifestyles, cultural practices and language), maintained herds of horses, cattle, and other livestock, lived in wagons covered by tents, and roamed widely throughout the central Asian steppes during the Iron Age. They were amongst the first peoples to master mounted warfare, and they developed exceptional equestrian skills as well as pioneering the use of the composite bow whilst riding.
Historically and culturally, the influence of horses on these cultures was strong. This influence later expanded to encompass many civilizations and regions, and was particularly visible in cities and economies, starting in the 18th century through the early 20th century, before cars and other modes of transport replaced horse power.
In short; horses had a lengthy and profound impact upon the development and progress of human civilizations. But how has the horse been affected by people?
People have reshaped the horse through selective breeding and crossbreeding, as seen in other domestic animals and plants (more examples: here; here; here; and here). Human influence is captured in the genomes of modern horses in a number of ways: (i) extreme diversity in mitochondrial genomes, which contrasts sharply with a Y-chromosome that is virtually identical in all modern domestic horses; (ii) higher mutational loads than in wild horses from the Upper Paleolithic; and (iii) selection at genes involved in locomotion, physiology, development, and behavior (ref).
Although we no longer depend upon them as we once did, people still influence horses by selecting for specific traits, which is obvious as both the horse racing and horse showing seasons are regaining their annual momentums throughout much of the Northern Hemisphere. This raises the question whether ancient horse people also selectively bred horses to fit their particular needs? If so, what traits were they selecting for?
DNA from ancient horse fossils shows they were genetically diverse
Surprisingly, well-preserved horse fossils are quite rare, so it has been difficult to study genetic changes occurring during that critical time period when horses were being transformed by domestication. But several remote archaeological sites do have rich grave goods — particularly a number of exceptionally preserved ancient horses and their furnishings.
To explore how domestication has altered modern horses, molecular archaeologist, Ludovic Orlando, a professor at the Natural History Museum of Denmark at the University of Copenhagen, and Research Director of the Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) laboratory at University of Toulouse, and an international team of 33 scientists from 16 universities, sequenced and analysed the genomes extracted from a small piece of bone of 14 ancient horses excavated from three separate royal Scythian burial sites across the steppes (Figure 1A).
These horse fossils were between 2,300–2,700 years old, and the sites included Arzhan, in the Tuva Republic, where over 200 horses have been excavated, also Berel’, Kazakhstan, where no less than 13 horses were preserved in a single, permafrozen funerary chamber, and one 4,100 year-old mare from a site in Chelyabinsk, Russia, that belonged to the earlier Sintashta culture, which first invented two-wheeled chariots drawn by horses.
“With the exception of two horses, none of the animals were related,” said a co-lead author on the paper, horse geneticist, Pablo Librado, a post-doctoral researcher at the Centre for GeoGenetics at the Natural History Museum of Denmark, in a press release.
This lack of inbreeding suggests that Scythian horse breeders maintained natural herd structures and did not breed a limited number of valued lineages. It also reveals that the sacrificed horses came from widely dispersed populations.
“It fits with Herodotus’ depiction of Scythian funerary rituals, whereby sacrificed horses represented gifts from allied tribes spread across the steppes,” said Dr. Librado, noting that the horses excavated at Berel’ also wore a variety of harness ornaments.
DNA analyses reveal a diversity of coat color patterns within Scythian horses, including bay, black, chestnut, cream and spotted animals (Figure 1A), indicating that stallions with a variety of coat-color patterns were used in elite funerals.
Although they are widely viewed as warriors, the Scythians apparently were skilled horse breeders, too. For example, the team identified 121 genes selected by Scythian breeders, most of which are involved in the development of forelimbs. This indicates that Scythian breeders selected horses with strong legs.
Many — but not all — of the ancient horses carried gene variants associated with speed — the same gene variants found in present-day racehorses. But the Sintashta mare and four of the Scythian stallions were heterozygous for these genes and thus, probably were not as fast as racehorses. Further, the unexpected discovery of one gene in particular, the MSTN mutation that is associated with the enlarged muscles seen in modern sprinting racehorses, suggests that Scythian breeders were selecting animals with both speed and endurance.
The team found that Scythian horses did not carry the DMRT3 “gait keeper” gene mutation that is responsible for alternate gaits, so these horses were neither natural, nor speedy, amblers. (The amble is a gait that is slower than a gallop but faster than a walk.)
Not surprisingly, the Scythians selected gene variants that minimize water loss, an advantage in the arid steppes where daily water sources are scarce — and these are gene variants that, coincidentally, promote horse milking, which has been a common practice throughout the region for longer than 5,500 years.
Horses experienced a significant collapse in genetic diversity during the last 2,000 years
Although it is interesting to learn about the phenotypes of ancient horses, such as the coat color patterns and whether they were gaited, the genomic data provide a sobering look at the genetic cost of domestication for horses.
For example, it was recently discovered that a now-extinct lineage of wild horses existed in the Arctic until at least 5,200 years ago, and these animals significantly contributed to the genetic makeup of present-day domesticated horses (ref). Yet comparisons between genomes from Scythian horses and that ancient vanished lineage reveal that the Scythian horses shared more genetic diversity with the Arctic lineage than with modern domesticated horses. This shows that sometime within the past 2,000 years, equine genetic diversity collapsed. This loss of genetic diversity reflects ongoing changes in horse husbandry practices, which have moved towards maintaining fewer and fewer stallions, such that, today, almost all domesticated horses carry identical, or nearly identical, Y-chromosomes.
“Many Y-chromosome haplotypes co-existed within Scythian horse populations,” said co-lead author, anthropologist Cristina Gamba, who was a postdoctoral researcher at the Centre for GeoGenetics at the time of the study.
“The first three millennia of horse domestication thus preserved a large diversity of male lineages. It only vanished within the last 2,000 years.”
This depletion of Y-chromosome diversity was mirrored by a significant accumulation of deleterious mutations in the genome of modern domesticated horses: both the Sintashta and Scythian horses had lower mutational loads than those seen in horses today.
These findings directly challenge the idea that ancient horses were the product of a small number of stallions and a comparatively unlimited number of mares. They also highlight the severe reduction in the effective population size of modern horses.
On a more fundamental level, this study provided evidence in support of the neural crest hypothesis, which is sort of a “grand unified theory” describing the domestication process. Basically, this hypothesis proposes that tamer animals also possess a suite of physical traits, such as smaller brains, diverse coat colors or patterns, curly tails or floppy ears, that can be selected for.
The genomes of modern horses reveal the domestication secrets of ancient people
It’s interesting what can be learned about people by studying the genome of another closely-associated species — horses, in this case. For example, by studying the domesticated horse genome, the authors have unveiled important features of Scythian funerary rituals. But most important, the authors provide evidence to revise our understanding of how Scythians managed and bred their horses — practices that contrast sharply with contemporary horse husbandry.
“In this study we wanted to go beyond the myth of Scythians being aggressive warriors, drinking the blood of their enemies in skull mugs,” Professor Orlando said.
“We wanted to reveal the many facets of the exceptional relationship that these people developed with their horses.”
Pablo Librado, Cristina Gamba, Charleen Gaunitz, Clio Der Sarkissian, Mélanie Pruvost, Anders Albrechtsen, Antoine Fages, Naveed Khan, Mikkel Schubert, Vidhya Jagannathan, Aitor Serres-Armero, Lukas F. K. Kuderna, Inna S. Povolotskaya, Andaine Seguin-Orlando, Sébastien Lepetz, Markus Neuditschko, Catherine Thèves, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled Al-Rasheid, Stefan Rieder, Zainolla Samashev, Henri-Paul Francfort, Norbert Benecke, Michael Hofreiter, Arne Ludwig, Christine Keyser, Tomas Marques-Bonet, Bertrand Ludes, Eric Crubézy, Tosso Leeb, Eske Willerslev, Ludovic Orlando (2017). Ancient genomic changes associated with domestication of the horse, Science, 356 (6336):442–445. Published online on 27 April 2017 before print. doi:10.1126/science.aam5298
Pablo Librado, Antoine Fages, Charleen Gaunitz, Michela Leonardi, Stefanie Wagner, Naveed Khan, Kristian Hanghøj, Saleh A. Alquraishi, Ahmed H. Alfarhan, Khaled A. Al-Rasheid, Clio Der Sarkissian, Mikkel Schubert and Ludovic Orlando (2016). Review: The Evolutionary Origin and Genetic Makeup of Domestic Horses, Genetics, 204(2):423–434. doi:10.1534/genetics.116.194860
Mikkel Schubert, Hákon Jónsson, Dan Chang, Clio Der Sarkissian, Luca Ermini, Aurélien Ginolhac, Anders Albrechtsen, Isabelle Dupanloup, Adrien Foucal, Bent Petersen, Matteo Fumagalli, Maanasa Raghavan, Andaine Seguin-Orlando, Thorfinn S. Korneliussen, Amhed M. V. Velazquez, Jesper Stenderup, Cindi A. Hoover, Carl-Johan Rubin, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, David E. MacHugh, Ted Kalbfleisch, James N. MacLeod, Edward M. Rubin, Thomas Sicheritz-Ponten, Leif Andersson, Michael Hofreiter, Tomas Marques-Bonet, M. Thomas P. Gilbert, Rasmus Nielsen, Laurent Excoffier, Eske Willerslev, Beth Shapiro, and Ludovic Orlando (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication, Proceedings of the National Academy of Sciences, 111(52):E5661-E5669. doi:10.1073/pnas.1416991111
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Originally published at Forbes on 27 April 2017.