Dun factor identified - reveals surprises and confirms old suspicions

Finally I have the time and mood to write this post. Regarding the coat colour of Eurasian wild horses, historic reports give us a clue but are not always unambiguous. For example, there is room for interpretation what “tan” or “mouse-coloured” is supposed to mean, because the authors of former centuries certainly did not use the words in the sense of modern horse coat colour terminology. In previous posts, I summarized and analysed all historic texts on wild horse exterieurs available to me:

What theTarpan looked like

Westernwild horse exterieurs: what does the evidence actually say?

C.H.Smith’s description of the Tarpan

WereEuropean wild horses dun-coloured or not?

Due to the ambiguity of historic accounts, genetic research identifying coat colour genes from ancient DNA of predomestic horses provides substantial additional clues on the actual colour of European wild horses. The last one of the posts linked covers a crucial question. Previously it has been resolved that Pleistocene and Holocene European wild horses had both the Agouti A and a allele, which produce either a bay or black base colour. But these two loci do not determine the final colour that is expressed; the so-called dun factor works upon these two base colours, and produces the phenotypes bay dun (a colour that is certainly wild type since Przewalski’s horses and kulan-onagers show it as well), black dun (aka mouse dun, blue dun or grullo), plus the non dun versions of the Agouti colours. Sorrel is not relevant for us, because it is based on a mutation of the Extension locus that was seemingly not present in predomestic horses. The problem is that the dun factor was not identified until recently, so that the actual phenotype of these horses was not determinable. This table below shows all four possible colours based on the Agouti locus (never mind the leopard spotted, that’s another story) that I did for Wikipedia: 

Now, the dun factor has been identified in a paper by Imsland et al. a few weeks ago [2]. It was found that the Dun factor sits on a locus for the TBX3 transcription factor. Loss-of-function mutations on this locus cause developmental defects in humans and mice in the development of limbs, apocrine gland, tooth and genitals. This shows once again that “colour genes” are not only responsible for coat colour but a wide set of developmental factors (for more, see the Dedomestication series). The study used domestic horses, Przewalski’s horses, other equids and two ancient horses. One ancient horses is from Yakutia and 4,400 years old, while the other one is from Russia as well, but 42,700 years old. Now what is interesting is that the Dun locus houses three alleles: Dun (D), non-dun1 (d1) and non-dun2 (d2). Non-dun1 still shows vestiges of the wild-type markings, you can still see a dorsal stripe although the contrast to the surrounding hair is not that big. In non-dun2 horses, on the other hand, primitive markings are totally invisible. What is even more interesting is that non-dun1 was found to be a wild type allele too, besides Dun. The Holocene Russian wild horse examined was found to be homozygous for d1, so it might have been either bay or black in life (the Agouti locus was seemingly not tested, alas). The Pleistocene horse was found to be heterozygous D/d1. So that not only means that non-dun equines existed already back 43,000 years ago, but also that both these alleles were present in one population at the same time.

As an example for a d1//d1 horse, see this photo of an Exmoor pony that I took at the Exmoor Pony Centre EDIT: Exmoor ponies have been found to be d2//d2 according to the supplement of the study. Exmoor ponies are, as far as I know, neither a nor A, but At/At, causing a condition called seal brown or dark brown. This allele has not been found in ancient populations yet. So if I interpret this correctly, considering the Exmoor pony’s colour a fully wild type colour would be speculative. For a d2//d2 horse, see this Noriker on Wikimedia commons.

Additionally to that, a considerable number of the predomestic horses tested in Pruvost et al. were found to be heterozygous A/a on the Agouti locus as well. This might implicate that in many predomestic Eurasian wild horse populations could have displayed all four possible colour morphs at the same time, the dominant ones possible more frequently than others (bay is dominant over black, dun is dominant over non-dun).

Although I suspected that, I find it surprising. I was actually hoping that the identification of the dun factor gives us a correlation between dun/non dun and a certain geologic age or habitat type, because it would make sense according to the camouflage effects the different colour morphs have (dun intuitively seems more suited to open habitats while non-dun fits forested, bushy landscapes in my subjective perception). However, if it is indeed true that there is no regional and geological correlation between the alleles A, a, and D and d1, wild horses of the ferus subspecies would be the only large herbivores displaying more than one colour morph in one population. It has been assumed that the homogeneity of wild animals, especially prey animals, is due to selection by predators because single individuals being coloured differently from the majority of the herd might be more attractive. Based on the current data, predomestic horses seem to violate this suspicion (I consider it merely a suspicion, I don’t know if it has been tested empirically).

However, there is another equine species that is known for occasionally showing deviant colour morphs, the Plains zebra (see this post).

I have been collecting a number of wild horse depictions in prehistoric art. I am going to present and analyse them here when I have the time to. Art, of course, leaves a much greater room for interpretation than genetic data. 

The authors also consider it likely that the zebra coat pattern is an extreme expression of dun plus wildtype markings [2].

[1] Pruvost et al.: Genotypes of predomestic horses match phenotypes painted in paleolithic works of cave art. 2011

[2] Imslandet al.: Regulatory mutations in TBX3disrupt asymmetric hair pigmentation that underlies Dun camouflage colour inhorses. 2015.