Superficial similarity vs. the original genes

This is a though post today, but it addresses an important issue. It covers the question whether the aurochs-likeness of cattle resulting from “breeding-back” attempt is only superficial as a result of breeding or if it is true alikeness as a result of the original genes producing the original traits inherited from the aurochs. Or more precisely, if a trait is physically identical to that of an aurochs (f.e. horn shape, leg length etc.) in a “breeding-back” result, is it indeed produced by the same genes as in aurochs, and thus true originality, or produced by novel, domestic mutations and thus the resulting phenotype is just a mimic? 

As long-term readers and all those with a basic biologic knowledge will know, the “one gene one trait” scheme is too simplified. There are two categories of phenotypic traits: qualitative traits and quantitative traits. It is necessary for this post to look into the differences of these two categories. 

Qualitative traits are such that are regulated by only one or very few loci (genes) and thus are easily discernable and show a typical Mendelian heritage. Colour (or colour aspects) are a classic example for qualitative traits. 

Quantitative traits, on the other hand, are controlled by a large to very large number of loci and thus their inheritance and genetic background is less easy to determine. Body size in mammals, for example, might be controlled by hundreds or even thousands of loci, with a couple of dozens at least that have a more or less big influence. For more on the genetic background of visible traits go here. 

Taking colour as an example, we know that in canines the nucleotid sequence of the Agouti allele causing the wildtype canine colour scheme is identical in coyotes, jackals, wolves and wildtype-coloured dogs. These four canines therefore all have the same allele for the same colour scheme. Thus, we can assume that when cattle have a “flawless” wildtype colour scheme, the alleles responsible for this colour is probably identical to the alleles the aurochs had, and thus the similarity is authentic and not just superficial (except for the chance that some mutated new alleles might have exactly the same function as the wildtype alleles, f.e. red pigment production). This goes for breeds with an authentic wildtype colour scheme, such as Maronesa or some Lidia, Heck and Corriente populations. A check for the alleles on the original loci in these breeds and comparison with aDNA from aurochs might confirm this if executed. 

For quantitative traits, the situation is much more difficult, also because the loci responsible for traits such as body size, horn size, horn curvature and others have not been determined yet, let alone the individual alleles with their individual effects. For example, let us assume that horn size is affected by loci that, with their wildtype alleles, produce oversized horns that are compensated by alleles that shrink the horns down again, so that in combination all the loci result in the horn size we see in the aurochs. Some domestic cattle might have mutations that produce oversized horns (such as Watussi, for example), others have mutations that shrank their size down (for example in Angeln or Murnau-Werdenfelser). Now we have a Heck cow, Erni, here with mighty horns the matching those of large-horned aurochs specimen. 

The phenotypic size matches, but do the genes? Do all the loci have wildtype alleles producing the wildtype size or do the loci have domestic mutations that coincidentally produce the same phenotypic size? It happens that this cow is a mix of breeds like Angeln, Murnau-Werdenfelser and Watussi (I did not pick those breeds as examples for nothing). It is very likely that domestication produced quite a mess on those manifold loci regulating this quantitative trait, and that crossbreeding and the subsequent phenotypic selection resulted in a coincidental mix of both wildtype and domestic alleles that happen to produce the same phenotypic horn size as in the aurochs. This is, in my opinion, the most likely scenario. It is also possible that Erni’s horn size alleles are exclusively wildtype or exclusively domestic, although less likely. The same goes for body size. Taking Chianina, for example, we know that European mainland cattle were on average smaller than cattle today. Chianina is a breed whose trademark is its large size and it is actively selected for it, and it has an aurochs-like body size – it might have never lost its large size from its aurochs ancestors, or secondarily developed it due to selective breeding. If its size is indeed re-gained it might be the result of a cumulative effect for selection for large size that favoured wildtype size alleles, or the result of new mutations. We cannot know.

Additionally to that, we face the problem that incredibly many aspects of the morphology of an individual have a developmental background. These include skull shape, proportions, full size, soft tissue such as muscling and intestines, and probably also aspects of the skeleton such as height of the processus spinosi (“hump”) and many other factors. Development is the result of the timing and amount of signal molecules (hormones and transcription factors) which are itself regulated by regulator genes. Also here the question old vs. new allele with a coincidentally identical effect is not solvable. It might be the case that a new mutation on a regulator locus produces the same level of, f.e., corticosteroids, and thus the same phenotype as the wildtype allele. However, taking into account that development is a complicated fine-tuned process I do not consider such a coincidence that likely. 

However, looking at the body size and horn size example we get to the point where I personally say: I do not care that much about the answer to this question. It is not relevant for the work of “breeding-back” whether the alleles of quantitative loci are all wildtype or all mutated or a mix with a coincidentally phenotypically identical result. Whether or not a optic/phenotypic match with the aurochs is authentic or just superficial can probably be ascertained only for qualitative traits such as colour (actually, currently only colour), but that does not affect what “breeding-back” can achieve in the least.