What ancient DNA is telling us about the prehistory and history of the horse

Ludovic Orlando has a great review of recent research into the origins and evolution of domesticated horses: “Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics”. The review is open access in BioEssays.

Here’s a cool fact:

With nearly 300 ancient genomes sequenced at above onefold coverage, horses have provided the largest genomic time series characterized to date after humans.

I’m a bit surprised that dogs aren’t higher than horses, but horse bones are quite a bit more common in some archaeological settings.

Botai horses indeed did not show close genetic affinities to modern domestic breeds. They clustered instead together with the Przewalski's horse, a horse discovered in the late 1870s roaming wild in Mongolia, and considered since as the only truly wild horse living on the planet. In short, the earliest domestic horses known in the archaeological record appeared to be the direct ancestors of the only modern horse that was supposed to have never been domesticated. It then became obvious that current models of horse evolution required serious rethinking.

Instead, the ancestors of today’s domesticated horses appear in the archaeological record around 4100 years ago in Hungary. The date and subsequent widespread occurrence of this single lineage of horses is striking as a parallel to the spread of steppe ancestry in humans inhabiting the same regions. It would seem that the spread of Bronze Age steppe peoples brought a lineage of horses everywhere the people went.

The expansion of this population of domesticated horses is matched by the equally striking extinction of many diverse lineages of horses throughout Eurasia. The review suggests that additional lineages remain to be found, with hints of their existence given by the rare occurrence of very divergent mitochondrial DNA haplotypes in a few ancient specimens.

The review goes on to discuss several other issues related to horse genetics. One important topic is the introduction of progressively stronger inbreeding in the last 2000 years. Some societies selected for particular male patrilines, while others were more ecumenical.

Ancient DNA can cast an invaluable light into ancient phenotypes that are invisible from skeletal evidence. The most widely reported of these phenotypes so far relate to pigmentation. That’s not only because pigmentation phenotypes are highly visible, it’s also because they are genetically simple enough to enable reliable phenotype prediction from sparse SNP data.

With horses, there is a lot to go on for pigmentation analysis. Many well-known color variations exist today, and they differ within and between horse breeds. The genetic variants that correlate with many of them are known. The element related to pigmentation that Orlando includes in his review relates to a cultural pattern:

It is noteworthy that this information cannot only reveal the traits that past breeders most likely selected, but can also help document past funerary traditions. For instance, the analysis of coat coloration loci in the 13 complete horse skeletons found in the funerary monument of Berel (Kazakhstan) revealed that ≈2500 years ago already, Scythian Pazyryk Iron Age nomads herded the full diversity of horse coat colors present in the region today. Since those horses were specifically killed for the funerals of Pazyryk elite members, the genetic data also showed that sacrifices were not targeted toward particular family groups or coat colors.

Orlando here cites his own 2017 work in a paper led by Pablo Librado.

Overall it is a useful and interesting review. We are relatively advanced in knowledge of horse domestication now compared to many other domesticates, at least with respect to the major ancestors of today’s breeds. We have to keep in mind how much we don’t know about ancient variation that has not been sampled, and the discovery of presently-unknown populations should not surprise us.