Horse Genetics. Ernest Bailey

samples (aDNA) from horse bones at the Botai site in modern Kahzahkstan were tested to determine their relationship to modern horses. The results were surprising. DNA sequences from the Botai bones were not characteristic of modern domestic horses, but rather most similar to the modern Przewalski horses (Gaunitz et al., 2018). The conclusion from this study was that this particular domestication event involved the Przewalski horse species. Furthermore, very little of the DNA from these horses was found among modern domestic horses so this event did not contribute directly to the modern domestic horse. Therefore, although this was the site with the oldest physical evidence of domestication of a horse, it was not the domestication event leading to modern horses. The domestication event leading to the modern horse clearly took place elsewhere. The question remains open. We do not know why this initial domestication event failed. Perhaps cultural or political forces permanently changed the home range or agricultural strategies of the Botai people. It may be that Przewalski horses were ultimately found unsuitable for domestication. When the domestication of another species of horse succeeded, the Przewalski horse may have been abandoned as breeding stock. Indeed, Gaunitz and co-workers (2018) suggested that modern Przewalski horses are actually a group descended from the Botai population. Nevertheless, the DNA evidence shows that people recognized the value of horses and domesticated these animals in Botai about 5500 years ago. However, this event contributed very little to the genomes of modern horses.

      Other sites of domestication

      So, what were the origins of the modern domestic horse? A comprehensive study by Fages and co-workers (2019) entailed DNA sequencing and comparison of modern horses and archeological remains of horses from around Europe and Asia. They found evidence for the existence of four (possibly five) prehistoric species of horse. Today, only two species of horse remain, Equus przewalski and Equus caballus. One of the extinct lines was based on samples from Siberia while the other was based on samples from the Iberian Peninsula. These four horse species diverged from a common horse ancestor within the last 1 million years with limited gene flow between them before the Siberian and Iberian horses became extinct probably tens of thousands of years ago. The DNA sequences of the Iberian and Siberian horses are sufficiently dissimilar to that of the modern domestic horse that we do not believe the Siberian or Iberian horses contributed significantly to the modern domestic horses. The best candidate for origin of the modern horse may be from somewhere in central Eurasia.

      Genomic Data on Horse Evolution and Domestication

      What was the process for horse domestication? Once the idea of domesticating horses was launched, did people independently capture and domesticate local horses? Or were horses domesticated in one region and then spread around the world? Or might domestication have been a combination of the two?

      Earlier studies used DNA from modern breeds, compared the genomics of modern horses, and drew inferences about the domestication of the horse based on geographical distribution and genetic variation. Comparing the diversity among horses led to construction of phylogenetic trees, such as that in Fig. 1.1 (Chapter 1). These trees were very satisfying because they corresponded to what we know about the origins of these different horse breeds and their geographical distribution. We could also use genomics to investigate the relative contributions of mares and stallions. The cell has a small organelle called the mitochondria that is almost always inherited from the egg, therefore it is a measure of the influence of female bloodlines (Chapter 20). Conversely the Y chromosome is a male-determining piece of DNA and is a measure of the stallion’s influence, over many generations, on a population. Considerable diversity was observed for the mitochondrial DNA suggesting that many mares were recruited during the domestication process (Vila et al., 2001). Conversely, initial studies of the Y chromosome showed limited diversity. This led to the initial hypothesis that early domestication involved one or few males but many females. However, a beautiful hypothesis can be undone by future discoveries! aDNA studies painted a different picture.

      Although modern horses have limited diversity for the Y chromosome, aDNA studies showed that stallions had lots of diversity for Y until about 700–1000 years ago (Wallner et al., 2017; Wutke et al., 2018; Fages et al., 2019). About that time, it appears that stallions from the Middle East became popular in breeding programs throughout the world. One stallion must have been particularly popular and had a large impact on European horse populations. Extensive use of descendants of this stallion led to the modern disappearance of other Y chromosomes in most breeds. Only breeds in remote regions, such as Iceland, Norway, and North Eastern Asia preserved the ancient variants for the Y chromosome. At the same time, aDNA studies show a dramatic drop in genetic diversity among domestic horses for all chromosomal DNA during the last few hundred years reflecting rapid convergence of breeding practices and goals around the world. The modern domestic horse is profoundly different from the horses originally distributed around the globe.

      Domestication and selection for coat color

      Once horses were domesticated, people became adept at selecting them for the characteristics they valued. This is readily apparent when we consider the diversity of coat colors in horses. Since we have discovered DNA variants associated with coat color genes (Chapters 7–13), we can investigate the coat colors of prehistoric horses using aDNA. The results of these studies suggest that early horse breeders practiced selection for coat colors. Ludwig et al. (2009) observed that DNA tests from 14,000-year-old horse bones indicated that horses were uniformly bay in color. Around the time of domestication, 4000–5500 years ago, genotypes for both bay and black were found. However, over the next few thousand years there was an increase of horses with DNA sequences characteristic of the chestnut, tobiano, and sabino coat colors. Color variation among horses occurred coincidentally with domestication and was a probable basis for early selection by man of preferred breeding stock. One might suppose that the original color provided camouflage in the wild and protect horses from predators. However, people may have found flashy white markings or dilution variants attractive and selected those horses for their breeding herd.

      Summary

      • The evolution leading to the horse occurred almost entirely in North America, beginning 55 million years ago.

      • Following the evolution of the genus Equus in North America the species migrated across the Bering Strait and populated Asia, Africa, and Europe.

      • Equus went extinct in North America approximately 12,000 years ago but continued to thrive in Asia, Africa, and Europe

      • Domestication of the horse first occurred in Eurasia. However, aDNA testing proved that those horses were not the ancestors of modern domestic horses, rather, they were ancestors of a different horse species, the modern Przewalski horse.

      • The precise region, or regions, responsible for domestication of the modern horse is/are still unknown.

      • However, once horses were domesticated, it appears that early horse breeders practiced selection for color and other characteristics found in modern horse populations.

      References

Brown, D. and Anthony, D. (1998) Bit wear, horseback riding and the Botai site in Kasakstan. Journal of Archaeological Science 25: 331–347.

Budiansky,