Was sesame the Shiba Inu's original colour? What evolutionary genetics says

Sesame — the coat with hairs in alternating bands of dark and red pigment — is the rarest and most mysterious colour of the Shiba Inu. Many enthusiasts naturally think it is also the oldest: after all, it is the “wolf” pattern, that of wild canids. But evolutionary genetics tells a more surprising story. Thanks to the study published in 2021 in Nature Ecology & Evolution by Bannasch and colleagues, we know that the oldest colour in canids is not sesame — it is yellow/red, shared with white Arctic wolves and originated from a canid extinct over 2 million years ago.

The question that seems obvious

Those who know the basic genetics of colour in dogs know that the agouti wild type allele (aw) — the one that produces the alternating bands of eumelanin and phaeomelanin on every single hair — is called “wild type” for a reason: it is the pattern of wild canids. Modern grey wolves, coyotes, jackals — all have the agouti coat, the colour of those who live in nature and need to camouflage themselves.

The Shiba Inu is one of the most primitive dog breeds, separated from the domestic stock in remote times and isolated on the Japanese mountains for centuries. If agouti is the “original” colour of wild canids, and the Shiba is a primitive breed, then sesame — the expression of agouti in the Shiba standard — should be its most ancient colour.

Logical. But wrong.

Two million years before the wolf

In 2021, an international team led by Danika Bannasch (University of California, Davis) published in Nature Ecology & Evolution a study that rewrote the evolutionary history of colour in canids.

The researchers discovered that the ASIP gene — the same gene responsible for sesame in the Shiba — is not controlled by a single mutation but by two independent regulatory modules: the ventral promoter (VP), which controls the colour of the lower parts of the body, and the hair cycle promoter (HCP), which controls the dorsal pattern. The different combinations of variants of these two promoters produce five distinct colour patterns in dogs: dominant yellow, shaded yellow, agouti, black saddle and black back.

The surprise came from the phylogenetic analysis. The haplotype of dominant yellow — the pattern with a predominantly yellow/red cast, the one of Golden Retrievers and yellow Labradors to be clear — is not a recent creation of human selection. It is shared with the white Arctic wolves of Ellesmere Island and Greenland, and its origin dates back to a canid extinct that separated from the grey wolf more than 2 million years ago, during the Pleistocene.

In other words: the yellow/red colour in dogs is older than the grey wolf itself. It was not born from domestication — it was already there, in a common ancestor, millions of years before the first humans domesticated the first dog.

And the agouti? Isn’t it the oldest?

The agouti (sesame) is indeed the most common pattern in modern grey wolves — but “most common today” does not mean “oldest”.

The Bannasch study demonstrates that the colour of modern wolves (agouti, with bands on the back and a light belly) is the result of a specific combination of promoters (VP2 + HCP2) that stabilised in the grey wolf. But the HCP1 variant — the one that produces dominant yellow — is phylogenetically older: it comes from an evolutionary branch that separated before the modern grey wolf formed.

The evolutionary picture is therefore this: about 2 million years ago, an ancestral canid already carried HCP1 (dominant yellow). From that stock separated the branch that gave rise to the grey wolf, in which HCP2 (agouti) became predominant. When the first dogs were domesticated from wolves, they carried both variants with them — and human (and natural) selection then distributed the patterns differently in the various breeds and populations.

What it means for the Shiba Inu

In the Shiba, the four colours recognised by the standard — red, sesame, black and tan and white (cream) — represent four different combinations of the ASIP promoters:

The red is the dominant colour of the breed. Genetically, the red Shiba carry the combination Ays/Ays (two copies of the “strong” HCP1 promoter) or Ays/at — combinations that keep the concentration of Agouti high and produce predominantly red hair with at most a slight dark shading on the tips. The red of the Shiba is a version of dominant yellow/shaded yellow — the oldest pattern of all, the one that dates back 2 million years.

The sesame (in its variants sesame, red sesame, black sesame) is the expression of agouti with different shades. The classic sesame, with balanced bands of dark and red, corresponds to the agouti wild type pattern (aw/at) — the colour of the modern grey wolf. The red sesame, as we explored in the article on the genetic research to which our kennel contributed, is the Ays/at combination: one copy of the strong promoter and one non-functional, which produces that partial dark overlay on a red base that is its characteristic.

The black and tan is the at/at combination — two copies of the non-functional promoter. Without an active HCP on the back, the melanocyte produces only eumelanin (dark pigment), while the belly remains light thanks to the ventral promoter that works independently.

The white (cream) is not an absence of colour but a red with extremely reduced pigment intensity — genetically it is a red whose phaeomelanin production mechanisms are greatly attenuated.

In which of the three original populations did sesame live?

The three historical populations from which the modern Shiba descends — Shinshu (Nagano), Mino (Gifu) and San’in (Tottori/Shimane) — each had a predominant colour:

The Shinshu was predominantly red — the colour which, as we have seen, is evolutionarily the oldest. It is the population that contributed most to the modern Shiba, and with it red became the dominant colour of the breed.

The Mino was intense mahogany — a very dark and saturated red (sashige), probably a variant of dominant yellow with pigment intensification. Ironically, that deep red that defined the Mino is today considered a fault in the modern standard.

The San’in was predominantly black and tan (at/at) — the most “subdued” expression of the ASIP gene, without promoter oscillation.

And the sesame? It was not the predominant colour of any of the three documented populations. But this does not mean it was not present. The agouti (aw) is the wild type pattern — the “default” of wild canids — and in populations of primitive dogs not subjected to targeted artificial selection, one would expect to find it. It is likely that sesame was spread transversally across the three populations as a natural variant, but that it had never been the “typical” colour of any of them.

A historical confirmation comes from the book by Kengo Taniguchi “Inu no Nihonshi” (犬の日本史, 2012), which reports that the wild boar hunting dogs of the Kishu province had an official hierarchy of colours summarised in the saying: “一白、二赤、三斑、四胡麻”.

It is a classification of the colours:

and also from the 1964 book “Nihon no Inu to Ookami” (“The Dogs and Wolves of Japan”), by Hirokichi Saito, a monumental figure for Japanese dog fancying, among the founders and first president of the NIPPO.

The book reports that during the Tokugawa period (Edo), the homeland of the Kishū wild boar hunting dogs was the village of Taiji (near Shingu), corresponding to the current south-central region of the country, known as Kansai, and in particular it tells us that:

Saito then also adds a personal detail: among the excellent hunting dogs he had seen himself, many in fact belonged to the sesame (Goma) bloodline.

So sesame was already present, recognised and classified as a distinct colour in the hunting dogs of the period, but it was in last place in the colour hierarchy for purely functional reasons, not aesthetic ones.

In driven wild boar hunting, the hunter had to be able to follow the dog with his gaze in the woods. The white was the most visible, the sesame the least — because it is exactly the colour of camouflage. But this classification concerned the large game dogs (Kishu, medium size). For the small game dogs in the undergrowth — the progenitors of the Shiba — the logic was inverted: what was needed was a dog that the prey could not see, and sesame became an advantage.

The paradox is that the oldest colour, functionally suited to hunting in the undergrowth, was progressively disadvantaged both by practical selection (the large game hunters preferred white) and by the postwar reconstruction (concentrated on the Shinshu line, predominantly red).

Sesame survived not because someone selected for it, but because it is the wild type — the genetic default that re-emerges in the absence of a selective suppression.

Is the aw allele really “allochthonous”? Three objections

There exists a theory according to which the aw allele (agouti wild type, the one of sesame) would be an “allochthonous” gene in the Shiba — introduced by a cross with a small-sized Shikoku at an unspecified time. A suggestive theory, but one that does not hold up to analysis. Three objections.

First objection: there were no “breeds” to cross. As we have seen in the article on the three original populations, before the founding of the Nippo in 1928 there were no defined breeds. There were ji-inu — village dogs — distinguishable at most by size and place of origin. To speak of a “cross between a Shiba and a Shikoku” as if they were two breeds with defined boundaries is an anachronism: those categorisations did not exist. They were all local mixed dogs, and the aw allele could be present in any population without any need for “introductions” from another.

Second objection: geography prevented it. The Shikoku lives on the island of Shikoku. The Shiba — in its three varieties — lived on the main island (Honshu), in isolated mountain regions. The extreme geographic segregation of these primitive populations — the same isolation that made them distinguishable from one another — makes a casual cross between dogs of two different islands unlikely. It is not absolutely impossible (dogs travel with humans), but invoking a single cross as the origin of an allele widespread in an entire population is genetically naive.

Third objection: that is not how genetics works. The idea that a single mating can “insert an allochthonous gene” into a genetic heritage and spread it stably in a population is an excessive simplification. An allele introduced by a single outcross event is diluted by 50% each generation if it is not actively selected. To spread in a population, it must confer a selective advantage (natural selection) or be intentionally concentrated by the breeder (artificial selection) — neither of these conditions is plausible for a colour allele in an era in which no one selected for colour.

What science says: the study by Tanabe et al. (2001, Journal of Heredity), which analysed the genetic variability of East Asian dogs through microsatellite markers, divided the Japanese dogs into three genetic groups. The Shiba (both Shinshu and Mino) falls in Group C together with Kai, Kishu, Shikoku, Akita and Mikawa. The Okumura study then demonstrated that the crossing between Japanese breeds has historically been so intensive that individual dogs cannot be sharply distinguished genetically — which confirms that separating a “pure Shiba” from a “pure Shikoku” in pre-modern eras is an exercise without genetic foundation.

In other words: the aw allele does not need an “external” origin because there was no defined “internal” from which to distinguish it. These populations shared a common genetic heritage, the aw allele was already present in the ancestral stock of the canids (it is the wild type, the starting “default”), and its presence in the Shiba requires no special explanation — it is its absence in the red and black-and-tan dogs that is the result of selection, not the contrary.

The sesame paradox

There is a fascinating paradox in this story.

Sesame — the agouti pattern — is the “natural” colour of canids, the one that nature has selected for millions of years for camouflage in the undergrowth. And yet in the Shiba Inu, one of the most primitive and “natural” breeds among domestic dogs, it is the rarest colour.

The explanation is twofold. On one hand, the postwar reconstruction of the breed was based predominantly on the Shinshu line, which was predominantly red — concentrating the Ays variants of the HCP promoter at the expense of aw (agouti wild type). On the other, producing sesame correct according to the standard has been a challenge that many breeders preferred to avoid.

Here at Shinjukawa we were the first to import this colour into Italy and among the very first in Europe. Over the years we have specialised in sesame, producing only agouti sesame, and we are among the first to have obtained homozygous sesame — dogs that transmit the sesame colour with certainty to all their offspring, making possible a targeted selection that until a few years ago was unthinkable.

But today, thanks to some pioneers like Shinjukawa and the work of many passionate breeders, sesame is beginning to establish itself as one of the most beautiful and fascinating colours — a colour that reminds us that the Shiba, under its red coat, still carries the DNA of the wild canids that preceded it millions of years ago.

References

• Bannasch D.L. et al. (2021). “Dog colour patterns explained by modular promoters of ancient canid origin.” Nature Ecology & Evolution, 5, 1415–1423. — Key study identifying the origin of dominant yellow in a canid extinct 2 million years ago.
• Belyakin S.N. et al. (2022). “ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs.” Veterinary Sciences, 9(5), 222. MDPI. — Study to which Shinjukawa contributed biological samples.
• Kim K.S., Tanabe Y., Park C.K. & Ha J.H. (2001). “Genetic variability in East Asian dogs using microsatellite loci analysis.” Journal of Heredity, 92(5), 398–403. — Study classifying the Japanese breeds into three genetic groups, with Shiba, Kai, Kishu and Shikoku in the same Group C.
• Tanabe Y. (1991). “Phylogenetic studies of dogs with emphasis on Japanese and Asian breeds.” Proceedings of the Japanese Academy, Series B, 67, 133–137. — Fundamental study on the phylogeny of Japanese dogs.
• UC Davis Veterinary Genetics Laboratory. “Agouti (A Locus)” — 2022 update to the nomenclature of ASIP alleles based on the Bannasch study.
• Standard Nippo (Nihon Ken Standard & Commentary), updated spring 2024 — nihonken-hozonkai.or.jp
• Taniguchi K. (2012). “犬の日本史 — 人間とともに歩んだ一万年の物語” (The history of dogs in Japan: ten thousand years walking with man). Yoshikawa Kōbunkan. — Colour hierarchy of the Kishu hunting dogs (一白、二赤、三斑、四胡麻).