Origins and history of modern horses decoded

The domestication of the horse began relatively late in human history, around 5,500 years ago — long after dogs, cattle, and pigs. However, once humans began riding and milking horses and controlling their reproduction, the entire course of history changed profoundly. In particular, until the advent of motors in the first half of the 20th century, the horse transformed the way we waged war, travelled the world, and transported goods.

In a new article published in the journal “Cell”, an international team of 121 scientists reconstructs the complex history of the domestic horse. Not only do they summarise the transformations in the horse genome since the very earliest stages of domestication at a global geographical level, but they also outline the legacy of major equestrian civilisations through to the revolution of modern agriculture. The study employed cutting-edge DNA research methods to collect genomic data from 278 horse samples spanning the last 42,000 years.

Antoine Fages, lead author of the study, carried out the majority of the molecular work: "With the newly generated dataset, horses are now the animal species with the greatest number of characterised genomes after humans. This extensive dataset provides unprecedented insights into how the animal looked in the past, as well as how horse owners throughout human history have traded, mixed, or selectively bred their animals."

The scientists discovered that there was a previously unknown lineage of horses in Iberia until at least 4,000 years ago. This lineage no longer exists and contributed only marginally to the genome of modern horses around the world. The same applies to another horse lineage that roamed the vast expanses of Siberia from northern Yakutia to the Altai Mountains during the Upper Paleolithic and up until the third millennium BC. The study thus shows that, although there are only two main lineages of horses today — the domestic horse and Przewalski's horse — the available diversity of horse lineages at the time when humans first domesticated the animal was far greater.

Pablo Librado, who coordinated the bioinformatic analyzes, explains: "Iberia has a long tradition of horse breeding and very ancient cave paintings featuring numerous horses. The region was therefore proposed as a possible center of horse domestication. Our new genomic data shows for the first time that four to five thousand years ago, a previously undescribed horse lineage roamed the peninsula. However, they have disappeared and are not the ancestors of modern horses in Iberia or the rest of the world.“

An earlier study by the Orlando team, published last year in the scientific journal “Science”, showed that Przewalski's horse descends from a lineage that was first domesticated in Central Asia during the Chalcolithic period around 5,500 years ago (see http://science.sciencemag.org/content/360/6384/111.full). However, according to the study, the modern domestic horse descends from a different genetic lineage that spread across Eurasia during the Early Bronze Age until the end of the third millennium BC. The newly generated genetic data now helps to determine how this new lineage has evolved since then and diversified into the hundreds of modern breeds we know today.

Orlando on this: "Throughout history, humans and horses have shared a unique and reciprocal relationship. Not only were the outcomes of great historical battles decided on horseback, but in the 19th century horses were also of crucial importance to the economic life of major cities such as New York, London, and Paris, where they transported extraordinary quantities of people and goods every day. Our primary goal is to understand how humans and their activities have purposefully transformed the horse throughout history, which horse breeds were developed by various cultures and how many, and how these in turn influenced the course of human history.

The only horse breeds alive today that are genetically close to the horses that populated the continent during the Iron Age and the Gallo-Roman era are now found only on a few British islands and in Iceland. These were most likely brought there by the Norsemen. On the European mainland, however, a different group of horses, originating with the Persian Sassanids, became so popular that it gave rise to most of the modern breeds found throughout the world today. This influence was not limited to Europe, but also took hold in Central Asia.

In order to identify the factors underlying the growing success of this type of horse, researchers examined the genomes of Byzantine horses descended from this new type. They found signatures of positive selection in no fewer than eleven genes involved in the development of body structure, present in two clusters of HOX genes. This suggests that the morpho-anatomical characteristics first acquired in the horses of the Persian Sassanids were increasingly valued and disseminated following the Persian Wars and the Muslim expansion.

In addition to detecting changes in the morphoanatomy of the horse, the researchers were able to use their extensive genomic time series to track the frequency of specific gene variants underlying important traits of the horse, such as coat color, speed, or gait. The authors show that a number of gene variants associated with racing performance increased in frequency over the last 1,500 years. The first occurrence of the DMRT3 ambling gait gene variant was found in a specimen living in the late Middle Ages and increased in frequency over the last few centuries. This suggests that selection for motor changes relating to speed and gait took place mainly during the last millennium.

The most striking signal identified by the researchers, however, does not lie far back in history. Instead, it leads directly into the modern era. Prof. Orlando adds: "Our most striking finding was that the genetic diversity of horses remained relatively stable for most of the last four millennia. In recent centuries, however, this diversity declined markedly, coinciding with the development of closely related stud farms and modern breeding methods.“

This is perhaps the most important finding of this study: the modern world in which we live can barely give us a sense of the diversity of breeding resources that were available in the past, even just a few centuries ago. This calls for further multidisciplinary research incorporating history, archaeology, and ancient DNA, aimed at understanding the true evolutionary origins of modern domesticated animals and plants.