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Starting at the beginning – the process


So if we started at the beginning, with the horse before he was domesticated, we would be looking at an animal with a coloration much like the Fjord pictured above. The similarity between this particular type of bay dun and the coloring of wild equids is obvious, and was noted before the founding of the science of genetics. In his book The Variation of Animals and Plants Under Domestication, Darwin noted the primitive nature of this color.

[the similarity of color] in duns, of leg-stripes and of double or triple shoulder stripes… indicate the probability of the descent of all the existing races from a single, dun-coloured, more or less striped, primitive stock, to which our horses occasionally revert. — Charles Darwin (1896)

With the rediscovery of Mendel and his laws of inheritance, color variations came to be spoken of as “factors”, and then later as “genes”. Understanding physical reality behind these “factors”—the discovery of DNA—was still the better part of a half-century away. So a horse like this Fjord would have been said to have the “bay gene” and the “dun gene”. Much of how non-scientists talk about animal color still sounds like this. But within the scientific community, where advances in technology have given incredible insight into the mechanisms controlling development, color is spoken of as a process. A very complex and (at the moment) only partially understood process.

Let me try to give a simplified explanation of this developmental process and how it applies to bay dun.

Step 1 – Setting up for production

The precursors to pigment cells originate in the neural crest of the embryo. From there they migrate outward from the dorsal line, and multiply across the rest of the body. Once at home in the skin and hair follicles, these become the “factories” where pigment will be produced.

If you break something in this part of the system, you get spotted* phenotypes. The reason white patterns tend to trump all the other color traits—why, for instance, a dorsal stripe does not continue on through and bisect the white area of a tobiano—is that this is the start of the process. What happens within those cells after they start making pigment doesn’t matter if the cells never make it to a given location. Although horsemen, and certainly artists, tend to think of white as something added over the top of the basic color, understanding that color-producing cells have to migrate across the body makes it more obvious that white markings and patterns are actually the areas that those cells did not reach.

When pigment cells fail to migrate to the end of the limb, the result is a white marking on that leg.

Step 2 – Make the “factories”

Those pigment cells, once in place, are where melanin is produced. This process, which involves numerous steps, is known as melanogenesis. If you break something in this part of the process, the body may have viable pigment cells, but their ability to make pigment is compromised. Dilutions like cream, champagne and silver are mutations to (well-known) genes that control some aspect of melanogenesis, and the fact that different genes govern different parts of the process is why the phenotypes are different.

Step 3 – Regulate the product

Pigment cells also regulate the chemical composition of the melanin, which determines whether black (eumelanin) or red (pheomelanin) is produced. This is what was discussed in the series of posts on pigment-type switching, which is the proper term for this part of the process. If you break something in that part of the system, you change the proportion of red and black hair.

Step 4 – Maintain production

Because hair and skin are routinely replaced, pigment cells must continue to function to maintain coloration. If something in this part of the process is broken, there is a progressive loss of color. Greying is probably the most familiar example of an alteration that occurs in this step.

How this makes bay dun

So back to our domestic horse ancestor, who was bay dun. That first part, his bay “base” color, is determined in the process explained in Step 3. Back when colors were still “factors”, two major controls were theorized: Extension and Agouti. In modern terms, the theorized “Extension” is a gene known as MC1R and “Agouti” is a gene known as ASIP.  Together those two sites form the primary control of pigment-type switching in horses. In their original, unmutated form, they work together to give a pheomelanic (red) body and eumelanic (black) points. That is what is meant by the statement that “bay is the ancestral (base) color of horses”.

Because the pigment-type switches were formally identified first, it was possible to confirm that bay was the original wild color for horses. The assumption was that the ancestors of the domestic horse were also dun, but dun proved more elusive to identify at the molecular level. Part of the reason for that was that it was not in an expected place. In fact, it was not found in the expected part of the process. Because dun is thought of as a dilution—indeed the phenotype is diluted in appearance—the assumption was that the cause would be found in one of the sites known to be involved in melanogenesis (Step 2). In the paper I linked to in the previous post, the MLPH gene was examined and ruled out. That gene is involved in Dilute (d) coloration in dogs (often called “blue”), but had not yet been linked to any of the diluted phenotypes in equines, so it was a logical candidate.

But dun was found in a gene known as TBX3, which was not previously known to be involved in pigmentation at all, and the part of the process was not in the production of pigment but in the placement of pigment cells when hair follicles are formed. That’s back in Step 1. Hairs from the diluted areas of a Dun (D) horse have pigment asymmetrically distributed, so that the sides (viewed in cross-section) are unpigmented. It is that placement of the pigment on the hair shaft that gives the impression of paler hairs. In her dissertation on the topic, the lead author Freya Imsland describes the situation with Dun this way (emphasis is mine):

The precise nature of the reduced pigment intensity in Dun is highly unusual; it can in essence be described as a microscopic spotting pattern, whereby the pigment distribution within each hair is radially asymmetric.

She reiterates this explanation in the abstract for the dissertation:

This results in a microscopic spotting phenotype on the level of the individual hair, giving the impression of pigment dilution.

The timing of the mechanism behind Dun explains why, unlike cream or silver dilutes, dun horses have diluted bodies regardless of their base color. It is the placement of the pigment cells in the hair follicle, and not impaired production of pigment, that make the coat lighter in those areas. And that happens before pigment is made or pigment-type determined. That may also explain why Dun characteristics (like the dorsal stripe) persist even when the color is paired with subsequent dilutions.

The discovery of a new role for an established gene is an important scientific discovery. As people interested in horse color, we tend to think of discoveries like Dun in terms of tests (or more accurate versions of existing tests). But the investigation into Dun is a good reminder that when it comes to the process by which animals acquire their color, there are is still much that is left to discover, and that some of it may be surprising. Another interesting aspect of this discovery is that the idea that dun hairs were different at the microscopic level is not entirely new; this idea was suggested in older books on horses color (Geurts, 1973 and Green, 1974). This also has intriguing implications for the type of color-shifting seen in some of the traditional (large-scale, as opposed to “microscopic”) spotting patterns. But that is all jumping ahead, and a topic for another day!

How we got to here from there


So the original wild horses probably looked a bit like this Fjord, with pigment distribution causing a body color that was visually quite pale while the primitive markings were more intensely pigmented. But the color of the modern domestic horse is more typically pigmented at full intensity across the entire body, like the warmblood to the left. What changed? And why? The other big finding of the recent dun research was that this was a gradual process, and that it began long before—close to 40,000 years before—horses were domesticated. That will be the subject of the next post.

*Although it has been used by some horsemen for specific patterns, “spotted/spotting” is also the generic scientific term for any form of white marking or pattern.

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Pigmentation as a developmental process


I talked in a previous post about changing the framework of understanding for horse color from the familiar “base + modifiers” to one that is based on the evolution. In describing the original wild horses, I explained that their color, that color in all animals, is the result of a developmental process.

Their coloration was the result of a pigmentary process, controlled by a number of genes. While still in the wild, mutations to those genes changed part of that process, which in turn changed the color of the horses.

Since more time has passed since I posted that than I intended, and because it is so central to thinking about horse color from an evolutionary standpoint, I want to expand on this idea of colors as a biological, developmental process. We think of colors as traits—as aspects we can see in the individual or in breeding outcomes—but there is an underlying process involved. In any given species, that process produces a specific coloration known as the wild-type. You can think of it as the default setting for the species. In horses that default color is yellow dun: buff body coloring, black points and primitive markings. Using the “base + modifier” framework, we would think of this as “bay modified by dun”, but in actual practice this coloration is the result of many genes (known and not-yet-known) that control pigmentation as the embryo develops.

Now if you disrupt that development, if you change one of the genes that controls the process, then the outcome is different. That is what color mutations do; they disrupt some aspect of the process which in turn changes the final color of the horse.

And although this is a different way of looking at horse color, it is not completely unrelated to the more familiar framework. The way we tend to group modifiers corresponds with ways the process can be disrupted. Dilutions, for instance, disrupt the process of pigment production within the cells. White markings and patterns, on the other hand, disrupt the migration of those cells to parts of the body. (The difference between those two situations—cells that don’t work quite right and cells that are not there at all—is key to understanding the difference between forms of albinism and forms of piebaldism.)

So, just keep that in mind as we go forward with the next few posts. Our starting point is the original color of the species, which is a yellow dun much like the kind pictured at the top of this post. In the next post I’ll talk a little about the processes involved that produce that color… and then we’ll start breaking things (or at least muck them up a bit) and see what that does to the final color!

[For folks that would like to jump ahead and get a sense of how the different modifiers fit into the process of pigmentation, “Coat colours and mitochondrial lineages of ancient horses to document domestication” by Michael Cieslak has a wonderful graphic on page 14.]

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The Law of the Soft White Underbelly


In my previous post, I said that I would be following up with a post about dun. It occurred to me, however, that it might be helpful first to give some background on some terminology. There is no question that among those who like to talk about horse color, terminology can be a minefield. Some of that comes from the limits of the English language—there are only so many words for spotted—and some of it comes from the non-linear nature of discoveries. If only the pieces of the puzzle were found in order, or if we at least got to glimpse the picture on the puzzle box before proceeding, so we knew what the end result was supposed to look like!

But since that is not the case, terms get borrowed and repurposed and stretched to fit things. And in a sense, this is going on within each community focused on a particular domestic species. There is some back-and-forth, but with the rapid pace of discovery (and the ability of non-technical audiences to talk to one another about the subject, often without direct collaboration with the academic community) there is a certain amount of divergence. This can create inconsistencies that can lead to confusion for the unaware.

The conversation surrounding the new discoveries about dun have highlighted an instance of that kind of situation for those interested in horse color. The term that may cause confusion is countershading.

If you frequent online horse color discussions with any regularity, you have probably heard this term used to describe dorsal stripes on horses that were not true duns. But countershading has a very specific meaning when speaking of animal coloration. In fact, it is the subject of a scientific law. Thayer’s Law states that animals display darker coloring along their topline and paler coloring on their undersides as a means of camouflage, because it counters the shadow cast by the sun. My husband once referred Thayer’s Law as the Law of the Soft White Underbelly. It is why so many animals, like the wood mouse pictured at the top of this post, have pale undersides.

Abbott Thayer used this photo of a white rooster against a white backdrop to illustrate how shadowing on the underside of solid colored animal would make it more conspicuous. Meanwhile the pale undersides of the three ibexes in the second picture help to conceal them. 

Abbott Thayer was quite enthusiastic about his theory, and he tended to overstate just how pervasive this type of coloration was in the animal kingdom. It is certainly true that horses do not display this type of coloration in the same pronounced way that many other animals do. Writers have noted that strong countershading is not really a feature of horse coloration.

Externally, horses are recognizable by the long-haired tail; the mane that is both long and thick… and the poor countershading
The Genetics of the Horse, Bowling and Ruvinsky (2000)

Even so, cave paintings suggest that wild horse coloration followed Thayer’s Law at least to some degree.

Lascaux Cave Paintings - horse

We would call the color in the above painting mealy or pangare. In her book Farben und Farbvererbung beim Pferd, this is the color Henriette Arriens associates with the term countershading, and it is the equine color that most closely fits the scenario described by Thayer. It is, however, not a particularly common coloration in modern breeds. Outside of some of the heavy draft horse and rustic pony breeds, this type of pronounced mealy pattern is rather rare. In that it is much like the other primitive equine color, dun!

It is not hard to imagine that ancient cave painters were looking at horses with this type of coloration.

But the term has also been used by some authors for sootiness. In his book Equine Color Genetics, Philip Sponenberg refers to it as “black countershading”.

…the sooty effect is most commonly expressed over the top of the horse so that the back, shoulder, and croup can almost look black, whereas the horse is redder on the lower body, belly, and upper leg. This effect is called black countershading, or “sooty,” and results in an animal that is dark on top and lighter beneath.

This makes sense since the overlay of black hairs on sooty horses often reflects that same dark-on-top, light-on-bottom configuration. A countershaded bay, then, was a bay with an overlay of black hairs along the topline. This can be seen in some of the examples of sooty dappling on this Pinterest board.

This association with sootiness is probably why, when trying to distinguish the soft-edged dorsal stripes seen on some sooty horses from true dun dorsals, some began referring to markings like the one on the sooty buckskin below as “a form of countershading”. The idea being conveyed was that the marking was not related to dun, but rather was one way that sootiness (“countershading”) expressed on some horses. And since the term was so often used in online forums to argue that this or that horse was “not really dun”, for some the original connection to sootiness (never mind Thayer’s Law) was lost. Countershading was, for them at least, just another word for a non-dun dorsal stripe.


So when news came out that researchers looking for the causative mutation for Dun (D) had found an additional mutation for primitive markings “without any dilution”, quite a few people imagined that this second mutation was for “countershading”. There was confusion, however, that term did not appear in either the paper on the new discovery or the dissertation that described the research involved. That is because the scientific meaning of the term has not changed; it is still about a lighter underside countering the self-shadow of an object. Researchers may not be aware that some have given the term this different meaning, but even if they were, an audience of fellow scientists would likely be confused by the change. If the idea is to counteract the shadow cast by the mass of the body, a thin line of darker color along the back of a non-dun horse is not likely to provide much camouflage.

That is why the term is conspicuously absent in the scientific literature on dun. But I think there are other reasons why those of us who are not scientists might want to adopt some different terminology. I’ll talk more about that in the next post on the new not-quite-dun (d1) mutation.

And for those that have an interest in Abbott Thayer and his work on animal camouflage, check out “A Painter of Angels Became the Father of Camouflage.” I have a soft spot for him as another artist whose obsessive nature drew him into science (and the science of animal coloration, no less), but by any measure his work was incredibly influential. You can also access his son Gerald’s compilation of his work Concealing-Coloration in the Animal Kingdom (1909) through Google books.

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