Friday, 29 January 2016

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:

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. 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


13 comments:

  1. interesting! Maybe there could have been sexual dimorphism among wild horses? just a thought of mine....

    ReplyDelete
    Replies
    1. For Equus ferus ferus, I consider it extremely unlikely. The Przewalski's horse and all other living equines don't have sexual dichromatism, so it must have been the basal state, and the ancestors of domestic horses must have lost it secondarily again. Furthermore, the social structure of horses seemingly does not support sexual dimorphism, which is usually found in polygamic species but not equines where male and female live in the same herd.
      And if they was some kind of sexual dichromatism, it would not be related to the four colour versions suggested by genetic data, because those are just gene variants on one (respectively) locus and not sex-related.

      Delete
  2. My horse has countershading but tested d2/d2. So d2 horses don't necessarily have "invisible" markings.

    ReplyDelete
    Replies
    1. I think that countershading isn't included in "primitive markings" (dorsal stripe, shoulder and leg stripes), eventhough it is a wildtype trait.

      Delete
  3. Erst kürzlich wurde ein Bergzebrahengst, der ausschließlich Bay Dun Zorses (Zebra x Pferd) zeugte, genetisch untersucht. Dabei kam heraus, dass er tatsächlich Bay Dun ist. Näheres kann ich dazu leider nicht sagen, aber kontaktiere doch mal die Facebook Seite "Zorse Zuri" https://www.facebook.com/ZorseZuri/?ref=page_internal , dort wurde der Bergzebrahengst getestet.

    ReplyDelete
    Replies
    1. Dankesehr, das ist sehr hilfreich! Evolutionär macht es auch absolut Sinn.

      Delete
  4. Sorry, but I am not entirely in agreement with your conclusion. We are using two different DNA studies. The first study (Pruvost et al.,2011) analized (among other things) the DNA of predomestic horses of three specific moments: Late Pleistocene, Early Holocene and pre-domestic time (7,000-6,000 yr B.P.), of different samples of Siberia, East Europe and Iberian Pelinsula. The result was: In Late Pleistocene wild horses in Siberia and East Europe had only the Agouti A allele (there was no Iberian samples for this period). In Early Holocene Iberian wild horses had A and a alleles (there was no samples for other regions for this period). Finally, in pre-domestic time (7,000-6,000 yr B.P.) East Europe wild horses had and a alleles (there was no samples for other regions in this period)
    The second study talks about the presence of dun/non-dun1/non-dun2 in two specimens of Russia (Pleistocene) and Yakutia (pre-domestic time).
    With these two studys we can only affirm two things: 1-Eastern Europe pleistocenic wild horses were bay (non-dun1) and bay dun. 2- Siberian pre-domestic wild horse was non-dun1. I think the rest are theories, by now.
    My personal theory is that during the last glaciation the Iberian population were isolated. The prehistoric horse fossil record suggests a great genetic plasticity, so it´s not difficult to think that this population evolved. There are studies that contrast the great genetic diversity in Euroasiatic pleistocene horses with the genetic homogeneity in Iberian horses at this time. Euroasiatic horses adapted to the cold and Iberian horses adapted to a more temperate climate. The first time the black allele made appearance, was in the Iberian population. I think it was a trait that was an advantage for more wooded environment. When the glaciation ended and the forest comed back, this trait was extended. And yes, maybe there were the 4 (or 5) colors at this time.

    ReplyDelete
    Replies
    1. Yes, I went into that in a more recent article, thanks.

      Delete
    2. Ah, ok! You have a great blog. Thanks for all the information.

      Delete
  5. Please, see that picture: https://goo.gl/images/XLmmfJ
    It's from the article "Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses". I can´t find a link where I could read the full article for free, but this image makes you think that a black horse with non-dun1 gen shows a slight pale colour. If this is true, this would mean that there were no wild horses with a pure black phenotype, but dark dun-like. This has more consistency for me. I don't know any runner herbivorous with a pure black coat, not even forest herbivorous.
    What do you think?

    ReplyDelete
    Replies
    1. Not directly, both the d1//d1 and d2//d2 have a brown base colour, while the D//D has a black base colour. The d1//d1 condition does not conflict with a black phenotype as far as I understand.

      Delete
    2. Ok, I could read the full article. You are right. But the study is about prehistoric samples from Central and Easthern Siberia, not from Europe. Some evidences suggests that Europe's specific conditions generated phenotypic differences between European and Siberian wild horses: The Leopard pattern in Pleistocene and the black coat color in Iberian Early Holocene. These environmental factors could also influence a greater or lesser frequency of Dun color, so I think it would be necessary to study the Dun gene in European samples. But maybe I'm missing information.

      Delete
  6. This comment has been removed by the author.

    ReplyDelete