The colors of all wild animals are a tradeoff between camouflage, which hides the animal from its predators or hides the predator from its prey, and display, which involves making the animal more attractive to members of the opposite sex or more threatening to rivals of the same sex. In equines, camouflage may involve blending into the herd (as in zebras) or blending with the background (often dry grass.) Bay, black and chestnut are not very good camouflage colors, but flatter, duller shades of these colors are.
The dun gene flattens and dulls the coat color over most of the body, sometimes leaving head, lower legs, and manes and tails darker than the body. Both red and black pigments are affected. It also produces a highly variable degree of striping of the coat. In general a dun horse will have a dark stripe running from the mane to the base of the tail, which in some cases continues down the center of the mane (dark mane center with light edges as in the Fjord horse) and tail. (Dorsal stripes do occur on other colors, but they are rarely unbroken from mane to tail.) In addition duns often have zebra-like stripes on the legs (especially near the knees and hocks.)
Less commonly, they will have spiderweb-like markings on the forehead, or a cross stripe over the wither area—a marking common in donkeys. All of these markings are grouped as primitive marks.
One early study of dun suggested that the dulling is due to a crowding of the pigment granules to one side of the hair. My own observations tentatively support this, but I am aware of no published studies—looking at individual hairs under a microscope doesn’t seem to be popular today.
Dun is thought to be the wild-type gene for horses, and it is definitely dominant to non-dun. Why do we think it is the wild-type gene?
First, cave paintings. Almost all show the darker head typical of dun, and some also show other primitive marks. Cave artists were limited by the available pigments, but their renditions are certainly compatible with the various types of dun.
Dun, though a dominant gene, is not that common in most horse breeds today. Why? During domestication, an occasional mutation to non-dun must have occurred. Human beings are attracted to what is different, and the earliest domesticators of the horse probably prized these intensely colored variants—to such a degree that in many horse breeds of today dun is either non-existent or very rare.
The words dun and buckskin are rather loosely used, and often treated as synonyms. Genetically, however, it is better to reserve buckskin for a bay with one cream gene at the cream locus, and dun for the whole suite of colors produced by one or two doses of the dun gene. The colors include red dun (dun on a chestnut background) various shades of tan with black mane, tail and lower legs known as zebra dun, (dun on a bay background) and various shades of dark slate gray to tan to silver with dark points known as grullo (dun on a black background.)
In my science fiction book, Tourist Trap, I have both wild horses assumed to be descended from some transplanted from Earth during the Pleistocene, described as striped duns, and a domestic mare, Raindrop, whose base color is grulla (feminine form of grullo.) Those striped duns are assumed to be duns of various base colors with very strong primitive marks. I might add that Raindrop’s color and markings correspond almost exactly with those of the foal in the last picture.