Ancient horse colors - sekelsta/horse-colors GitHub Wiki
Before domestication
The oldest known coat color of horses was bay dun. Even today, the only surviving wild horse, the Przewalksi's Wild Horse or takhi, is consistently bay dun. Bay dun is a tan or sandy light brown color, with a dark stripe down the back from the end of the mane to the start of the tail. The stripe and certain other markings are called "primitive markings" because of how old the dun color is. The mane, tail, and lower legs are black, as they are in bay horses.
Over 42,700 years ago, there was a mutation to the dun gene which partly lost the dun color to create darker colored horses. It is called non-dun 1, and it changes the body color from the light brown dun to the much deeper brown color seen in bay horses. Non-dun 1 horses still have the stripe down the back like dun horses do. So at this point, there were bay dun horses as well as bay horses with primitive markings.
The leopard complex is another mutation from prehistory which can cause a variety of patterns from varnish roan to dalmatian-like spotting. Remains of horses from the Pleistocene have been DNA tested and 4 out of 10 of them were found to have the leopard complex. Cave paintings at Lascaux show leopard spotted horses, which makes it seem likely that both the leopard complex and pattern 1 are at least 25,000 years old. A full leopard pattern may have been good camouflage during the ice age. At this point there would still have been bay dun and bay with primitive markings as before, but on top of that some horses likely had patterns such as varnish roan, leopard, spotted blanket, snowcap, and fewspot.
Horses from 6,000-7,000 years ago, shortly before domestication, have been DNA tested and found to have a at agouti. This was especially common in Eastern Europe and the Iberian Peninsula, where in some cases the a allele (for black) was even more common than the A allele (for bay). This would allow horses to be grullo (dun on black) or black with primitive markings, along with bay dun and bay with primitive markings from before. Of course any horses with the leopard complex could also have had one of those patterns on top, though the leopard complex may have been less common at this point. The researchers think the black color may have blended in better with the dark forests which were spreading at the time. Interestingly the tarpan is an extinct wild horse from the regions where black and grullo seemed to be more common, and indeed it was mainly grullo. Yes, it's possible to see the primitive markings on black, see figure A here, where the middle horse is black with non-dun 1.
So before domestication, there would have been bay dun, grullo, bay with primitive markings, and black with primitive markings, as well as the leopard complex patterns. Many of the colors that are common now have not been found that far back, including chestnut, bay without the dark stripe down the back, and black without the dark stripe down the back.
After domestication
In many species domestication comes with an explosion of new colors, and horses are no exception.
The chestnut color and the sabino and tobiano patterns have been found in horses from the Bronze Age. Tobiano is at least 5,000 years old, as it was found in a horse from Kazakhstan 3654–3630 BC, around the time of horse domestication. The chestnut mutation was first found in horses from 3,000-4,000 BC (5,000-6,000 years ago) in Siberia. Sabino 1 was found in a horse from 2500-3000 BC in Siberia, so it's at least 4500 years old.
It's unclear when the now very common non-dun 2 mutation first appeared, as there was no test for it when some of these studies were done, but it's estimated to be a few thousand years old. Once it appeared, it would be the start of common modern colors such as the normal bay, black, and chestnut, without a dark stripe down the back.
The oldest silver dapple horse found lived around 800 BC in Siberia. The first sign of the cream gene was a buckskin horse from about 600 BC, again in Siberia. The gray mutation is also thought to be thousands of years old. Pearl was detected in a horse from 400-600 AD Germany, though it was heterozygous so the dilution would not have been visible.
For more info read:
Coat Color Variation at the Beginning of Horse Domestication - This is mainly useful for colors that appeared after domestication
Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art - more detail about the age of the leopard complex mutation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731265/ - includes info about the age of the alleles at the dun gene
Spotted phenotypes in horses lost attractiveness in the Middle Ages