(Eurasia) approximately 5500 years ago. Before domestication, people routinely hunted and slaughtered horses for food (Levine, 1999). However, bit wear on teeth from the Kazakhstan sites indicated that horses may have been ridden, an activity that is unlikely without domestication (Brown and Anthony, 1998). Mares’ milk residue found associated with pottery also strongly suggested that these horses were accustomed to human contact, as wild animals are not easily milked (Outram et al., 2009). Archaeologists continue to look for physical evidence of horse domestication in other parts of the world, however, some of the most interesting contributions to this topic have come from molecular genetic studies of DNA recovered from skeletal remains. In the case of the Botai horses, the DNA results produced a surprising twist to the story of horse domestication.
Ancient DNA
Since the skeletal remains of equids are often incomplete and therefore difficult to assign to a specific species (horse, donkey, zebra, etc.) the study of DNA in skeletal remains has been a boon to archaeology. At the time of death, the organic material in the body begins to degrade. However, DNA found within bone is often protected from harsh environmental exposure and may be recovered and sequenced after thousands of years. These types of material are called ancient DNA (aDNA) and their survival depends upon favorable environmental conditions such as freezing in permafrost, mummification, desiccation of remains, or simply burial in soil that is low in acid and lacking other elements that degrade DNA. Successful study of aDNA in the laboratory requires a very clean environment to avoid contamination with modern DNA, complex corrections for naturally occurring chemical changes, as well as sophisticated computer analyses (bioinformatics) to factor out contaminating DNA sources such as bacteria or plant material that may have been present at the burial site. Horse remains are plentiful in the archaeological record. The quality of DNA recovery is correlated with age and aDNA is routinely recovered from samples that are hundreds of years old to tens of thousands of years old. The record for the oldest ancient mammalian DNA sequence ever reported is from a 700,000-year-old horse (Orlando et al., 2013).
Which horse species was first domesticated?
DNA 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
