Wednesday, 31 October 2018

Is "genetic breeding-back" possible?

It has become en vogue in contemporary “breeding-back” to claim that their project also involves “genetics” or is based on genetic information, executing “breeding-back” not only on a “phenotypic” basis but on a “genotypic” level, which should lead to a more authentic result. The argumentation is that the original “genes” (simplified language, actually we are talking about alleles) of the aurochs have not been lost during domestication, but split up and mixed with domestic mutations among the modern domestic cattle populations. The goal of “genetic breeding-back” is therefore to trace down these genes among modern cattle and to unite them by crossbreeding and selective breeding in one population. Basically the same as with morphological traits, but more in-depth and concerning the whole organism as genetics are the key determinant for all biological aspects. Therefore, this method should lead to an approximation of the original aurochs and not a mere morphological double. This is the theory, and what some projects claim or claimed to do. 
But this is a scenario communicated in press releases. In order to see how much of that is in line with what is to be expected in a fact-based approach to the subject requires to have a look at the following questions: Where do aurochs and cattle differ genetically? Is it likely that domestic cattle preserve all the genetic material of the aurochs? Has the aurochs gene material been traced down in modern day cattle? Do any projects actively execute selective breeding on this genetic material? 

This is not a discussion where we can rely much on “hard facts” given in peer-reviewed publications but much of it depends on interpretation, predictions and deductive reasoning. This post presents my personal take-on to this subject so it is merely my personal opinion, but I give reasons for every statement (and, if necessary, also literature references). In short, I think the answer to the questions above is rather disillusioning concerning the possibility of executing “breeding-back” on a genetic level. 

Problem 1: Where do aurochs and cattle differ genetically and are all aurochs genes still alive?

First off, we have to elaborate where aurochs and cattle will differ genetically. The complete genome of a British aurochs has already been resolved, and a comparison to modern cattle has shown that apparently selection on genes evolved with milk production has taken place1. This is not surprising, but only the tip of an iceberg. Domestication alters the whole organism and these changes are morphological, developmental, behavioural, endocrinologic and genomic. Not only some new mutated alleles such as for new colour variants popped up during domestication, it altered the development of the whole organism. The timing of the ontogeny has been affected, some developmental changes are stopped in the process (see paedomorphy), others speeded up (see earlier maturity). These changes are caused by genes regulating endocrinologic system (in essence, much of the ontogeny of an animal is regulated by endocrinology) and the nervous system and there is a mutual interplay of both. An organism is one functional entity and you cannot look at just one aspect only. These genes probably cause most of the fundamental differences between a domestic animal and its wildtype in development, morphology and behaviour. New mutations directly affecting morphology, such as new colour alleles, play a role as well of course. How many genes are we talking about in total? It is hard to give a precise number or only an approximation as those particular genes involved in all these developmental, endocrinologic, neurological, and morphological and their individual function have not been identified yet. But the number might be very or even very, very high. For comparison, body size in humans is suspected to be influenced by about 50 loci (genes) alone that have a more or less significant impact on this one quantitative trait according to  Visscher 20082. Other sources give even way higher numbers like 6000 loci influencing the metric dimensions in mice3. Dobney and Larson 2006 write that the thyroid production, which affects many morphological aspects and produces typically domestic behaviour and morphology traits, is regulated by a “myriad of genes”5. So my personal estimate that the number of genes regulating all the developmental, endocrinologic, neurologic, and morphologic differences between domestic and wildtype, cattle and aurochs, might be hundreds, or even thousands of loci (even considering that pleiotropy and cascades probably play an significant role as well). 

As I wrote above, we are in a speculative area here as the individual genes and their exact functions in this complex interplay of factors that shape a living organism have not been identified. This is why publications only give approximations of numbers of genes that might be involved in examples such as body size. In short: we do not know on how many loci (genes) aurochs and cattle differ but they might or should be of considerable number. Furthermore, it has not been identified yet which those particular genes are. 

Aurochs versus domestic cattle: the defining key genes 
What are those studies allegedly comparing aurochs and cattle on genetic basis focusing on, then? For once, phylogenetic markers such as haplotypes. These are used for comparative studies to resolve phylogenetic relationships among species or groups of species and work well for this purpose. Phylogenetic markers are regions in the genome that are barely effected by selection and mutate on a certain rate so that they can be used for resolving phylogenetic relationships. Those include haplotypes on the Y-chromosome, for example, or mitochondrial DNA. In the case of cattle and aurochs, markers are useful when we want to determinate phylogenetic relationships of regional/chronological subgroups and clear up cases of introgression. But when we want to resolve how much and where aurochs and cattle differ on a genetic (and consequently organismic) basis, phylogenetic markers are not suitable because they do not involve the key genetic regions listed above. I think this is the actual misunderstanding in the debate. 
In the most recent publication on this issue, the SNP comparison between the British aurochs and a number of cattle breeds calculated after the Nei distance method, the study focused on about half a million Single Nucleotid Polymorphisms. SNPs do affect the phenotype, as the study itself writes, but considering that mammal genomes can have about 3 billion base pairs, you can do the math how much. Not only is the actual influence of these SNPs on the organism not that considerable, the very small sample size might also result in completely different results when another, and another, and another half a million SNPs are investigated. Breeds that score high in the one result might score low in the other results and so on. That goes as much for Pajuna as for Fleckvieh and even the outgroup Nelore. Furthermore, the Nei distance method is, in my opinion as a layman, not a suitable tool to describe the difference between aurochs and cattle or to resolve the population genetic evolution that has taken place during cattle domestication. I give my reasons for that thoroughly in this post. So the fact that Pajuna scores highest in this comparison does not justify the claim that it is closest to the aurochs in any way. Even though it is morphologically aurochs-like in a number of respects – but the chart obviously does not show a correlation between aurochs-likeness and high scoring anyway, which might also say something. 

Is it likely that domestic cattle preserve all the genetic material of the aurochs? 
No matter how many loci we are talking about, a quintessential question is whether or not we can expect that much or all of the original aurochs alleles are present among domestic cattle. To explain why I write of alleles now instead of loci: in the above section, the question was on how much gene locations (loci) aurochs and cattle differ. Cattle have two variants of the gene, called alleles, per locus. In domestic cattle, new alleles turned up due to mutations and replaced wildtype alleles. The question is to what extent and if, despite this fact, still all or at least most of the defining, influential wildtypealleles can be found within the modern cattle gene pool. By defining alleles, or key alleles, I am referring only to those alleles that were responsible for the organismic differences we see between cattle and aurochs. Cattle and aurochs probably also differed on a number of loci that did not have a considerable influence on the genotype but were just more or less neutral diversity or variation. These loci are not relevant for us in this discussion. Furthermore, it is not necessarily the case that all alleles that form the domestic phenotype are of novel origin. For example, some genes associated with large size in horses are of predomestic origin6. So it is possible that some domestic conditions on quantitative traits can partly also be the result of cumulative effects due to selection. This, on the other hand, does not increase the chance for all wildtype alleles to have survived in cattle. 

The evolution of domestic cattle from a population genetic perspective 
The scenario proposed by those who claim that indeed all or most defining aurochs alleles are to be found within modern cattle is one of a classic population fragmentation and genetic drift: the population becomes fragmented and split-up as it is spread, new alleles intermingle with wildtype alleles, genetic drift and fragmentation produce an uneven distribution of wildtype alleles among the new lines or clades that have been formed. Population genetics know this as the classic scheme of a fragmented and expanded population. While one population or breed might still have the alleles A, B, C, D, E, F, G, H, I, the other one might have J, K, L, M, N, O, P, and yet another one might have the alleles Q, R, S, T, U, V, W, X, Y, and Z among a quantity of new, domestic alleles. And genetic breeding-back should take these unevenly distributed aurochs-alleles and re-unite them in one lineage, or at least what is left of it. 
But this is not the evolutional process that domestic cattle underwent during domestication. At first, there was a dramatic genetic bottleneck event as the founding population of domestic cattle apparently was very small3. Then there was massive directive selective pressure that certainly altered the genotype as it altered pretty much all aspects of the organism (development, behaviour, immunology, morphology). And as the farm fox experiment has shown, these changes can happen quite rapidly, even within few generations4. It has to be assumed that the starting population of domestic cattle was more or less uniform for defining traits of domestic animals; all of them must have been domesticated in a similar manner, including modifications in behaviour (docility, agreeableness, trainability etc.) in morphology (meat, milk etc.) and those that go hand in hand with these changes as a result of pleiotropic effects and developmental cascades (for more, see the dedomestication series). I do not believe that the starting population of domestic cattle was heterogeneous on these traits in the sense that some had the right behaviour while others had a wildtype behaviour, some had an unaltered morphology and so on. Clearly the first domestic cattle were only half-domesticated at some point, but probably all individuals in a similar way. Some basic changes must have been universal to all of them. This is my main point: in the early phase, when wild aurochs were transformed to a domestic state, some key wildtype alleles must have necessarily been lost completely from the population as a result of the directive selective pressure and the more or less uniform result – more or less uniform only in the sense that all individuals of the populations are domestic in the same manner. Certainly some lineages were modified more drastically than others (and this is what we see very clearly in modern day cattle). But the basic alterations that made the animals domestic must necessarily have been universal among those early domestic cattle and still are today, otherwise not all of them would show the same kind of modifications. Consequently it is very likely that the process of domestication irreversibly eradicated some essential wildtype alleles. What happened after this early point were 8000 years of further evolution in human custody: reproductive isolation (more or less), selective pressure on certain phenotypic traits plus genetic drift. It is very likely that another number of key wildtype alleles has been lost or actively eliminated in this process. Or to be more precisely, I think it is highly unlikely that it would not have happened. 
It is clear that domestication is not some discrete step that is completed at some point. Actually, domestication is still an on-going, fluid process: we have numerous cattle lineages and breeds that are way more modified than others, each after a different purpose. In a sense, Fleckvieh is more domesticated than Maronesa, and Maronesa is more domesticated than the cattle of the first hundred generations in human custody (and probably way, way more domesticated despite its aurochs-like looks and hardiness). You could even say that by putting Holstein-Frisian bulls on a Sayaguesa herd or overbreeding highly derived breeds we are still continuing to domesticate the domestic cattle gene pool even further today. But that is not to say that there is a vivid chance of having all defining aurochs alleles still present in domestic cattle to an extent that allows to more or less restore the wildtype. I think that the population genetic processes this population underwent during the last 8000 years do not allow it, or at least make it very unlikely. 

The domestic cattle gene pool was not entirely reproductively isolated as there apparently was occasional regional introgression from wild aurochs. It seems that these introgression events contributed traits helpful for establishing the newly introduced domestic cattle in other regions (immunological and other alleles) and it would, theoretically, be possible that these introgression events reintroduced wildtype alleles previously lost during domestication. However, I think this is not plausible. Local aurochs might have contributed a few advantageous alleles, but it seemingly did not alter the integrity of the cattle as domestic animals. This is not surprising considering the selection policy the ancient farmers must have had: most likely they continued breeding with hybrids that showed increased robustness or whatever trait they considered advantageous, but probably not continued breeding with hybrids that were a throwback from the economic perspective (morphologic and behavioural adaptions shaped after man’s purpose). 

I am convinced that the 8000 years of domestication eradicated a lot of alleles that made the aurochs the wildtype animal that it was and were replaced by new alleles that make cattle the domestic animals that they are. All cattle on this world are domesticated in the same way, just not to the same extent. They underwent the same morphological changes (paedomorphy, reduced sexual dimorphism, reduced brain volume, altered body shape/muscling, proportions, intestine size) and the same behavioural changes (docility, agreeableness, trainability) and consequently also the accompanying neurological and developmental alterations. Not to the same extent in all cattle, obviously, but they are universally present among all domestic cattle on this world and so we have to assume that the genetic basis for these changes is so as well, and therefore that these have replaced the wildtype alleles on the involved loci. This fact plus the population genetic history of the 8000 years of domestic cattle evolution makes it very likely to me that many of the key wildtype alleles that shaped the wildtype organism called aurochs are lost entirely among domestic cattle. This is an assumption, and this assumption could be tested by a rigorous comparison of the now fully resolved aurochs genome with that of domestic cattle. 

Problem 2: Has the genetic material of the aurochs been traced down in modern day cattle? 

Even if the proposal that “all aurochs genes” are still present in domestic cattle and that no original alleles were lost bears any truth (which I am convinced is very, very unlikely), “genetic breeding-back” would require these alleles to be identified and to be located within modern day cattle. First of all, these alleles are not identified. Only some are, like colour alleles, and not even in this case it has been tested if the E+allele causing the aurochs colour scheme is really identical to the allele the British aurochs individual had (what if, for example, if such a test would reveal a surprise?). As the example with body size in mice and human shows (see the literature cited above) it is not even known in these well-studied model organisms how many loci are involved in body size. And this is just one complex trait. We cannot even dream of knowing the specific alleles responsible for all the developmental changes resulting in the domestic phenotype we see, we only speculate that they are there. And having those loci identified and alleles identified in aurochs and tracking them down in modern cattle, distinguishing them from domestic variants and even measuring the quantity to which they are present in which cattle clade or breed is just a few (illusive) steps further. Based on the literature we have, and even counting scientifically worthless press releases, apparently nothing has been done in this direction, not even a little bit. 
A number of cattle breeds have been investigated (but not for the important genetic factors explained above), but an important group of taurine cattle have not, probably for their difficult accessibility: Near-Eastern and North African rural cattle. Those cattle, although mostly short-horned and small, have a quite aurochs-like physique and might be less derived than European ones, perhaps also on a genetic basis. Furthermore, turano-mongolian cattle should not be ignored either as they apparently represent a distinct gene pool within the taurine branch on its own (see here). 

Do any projects select on this material?
Even if all necessary key aurochs alleles were present in domestic cattle (which is very unlikely and neither proven nor investigated) and even if all these alleles had been identified (which is not the case) and even if these alleles had been traced down and quantified in a representative sample of domestic cattle (which is not the case either), how would genetic selective breeding look like? 
At first, a set of cattle breeds would have to be chosen that has all includes all the desired wildtype alleles in sum, no matter how it is distributed among the breeds. It might be that you need only three breeds because one breed already has 50% of the alleles, another breed those 50% pls another 10%, and the last one the missing 40%, or maybe as much as twelve or 30 breeds (again, I think that such a scenario is as much as impossible anyway). You would have to know which breed has which alleles. Then you execute crossbreeding. The first generation is heterozygous in any case, so you neither gain nor loose something. In the second generation, however, you would have to check the genotype of the offspring and make sure that you continue breeding only with those that unite a higher portion of wildtype alleles than the individuals of the parental generation do. And so forth, until you have re-united all wildtype aurochs alleles in one genotype. Depending on how many loci you have to deal with you can do the math how long you have to carry out the breeding. I cannot give any number because we would need to know two things: 1) how many loci are relevant in total (as explained above, the number might be very high) 2) how much of the relevant loci with wildtype alleles are already shared in the set of breeds chosen. For example, if the breeds chosen share already 90% of the wildtype alleles, and you only have to unite the remaining 10% that are split-up among the breeds the work is less. This is all speculation, but just to give an idea about the selective breeding work that would have to be done let us do a simple calculation. Let us say the key genes where aurochs and cattle differ compromise 1000 loci (which might be a conservative estimation), and let us say that 90% of the wildtype alleles are already shared in the set of breeds chosen (which is high), the breeding would have to focus on 100 loci. This is a lot.

Are any of the current projects doing something anything like this? There is no hint in any press release of any project that they are doing something that would qualify as a precise genotypic selective breeding as described above. I also see no way how they could, considering that the necessary research work has not been done and that a considerable number of wildtype alleles are probably not present in domestic cattle anyway. If they are not doing that, what do they do?
The only project that is claiming that “genetics” are influencing or will influence their breeding choices and that has presented a little glimpse on what those “genetics” are is the Tauros Project. So far, the Tauros Project has presented a Nei analysis of a number of breeds comparing half a million SNPs to that of the aurochs. You see the resulting chart here. The project claims their chosen breeds (bold) score high – actually it looks like they are distributed quite evenly among the list, and the derived breed Fleckvieh scores high as well. The project writes further that the fact(?) that their chosen breeds score high is a confirmation that their choice criteria were right as they initially chose their breeds based on the “phenotype” and not genotype (which is funny since the project actually claimed to choose their breeds based on genetics in early years). 

As I wrote above, SNPs only have a minor influence on the organism as a whole, and so do haplotypic variations on phylogenetic markers. They are useful to resolve relationships between phylogenetic clades but not of much use when determining the organismic differences between a domestic animal and its wildtype. Furthermore, the Nei distance method is not the appropriate tool resolving the complex population genetic evolution that domestic cattle underwent but rather for a textbook example of simple population fragmentation. Thus it does not surprise me at all that there is no correlation between neither morphological primitiveness nor hardiness/robustness in the chart. Apart from that, a number of important or at least interesting types of taurine cattle have not been tested (Near-Eastern cattle, Turano-Mongolian cattle). To conclude that “genetics obviously do not matter” based on this fact would be the worst assumption to make and would show a lack of biologic understanding. Genetics of course determinate what the organism is going to be like, and genetics are of highest importance in animal breeding and in determining the differences between a domestic animal and its wildtype. 
What you see is an analysis of genetic material that is not of high relevance of the organismic aspects we are talking about, analysed with a tool that is not really appropriate for the evolutional process we are looking at. If you say “well, but it is the best we currently have so we have to go with that”, I can only counter that you have to be aware of the fact that the “best we have” in this case does not say much if anything. Thus, if the Tauros Project is indeed giving any importance to the “genetic similarity” in the form of SNPs or phylogenetic markers in their breeding policy and if indeed future generations of Tauros cattle by coincidence* score a little higher in this respect I honestly have to say that it would not impress me that much. I go even further: I predict that a domestic cattle population that is even identicalon all of the half a million SNPs and phylogenetic markers (that is, neutral variations on gonosomal or mitochondrial sequences) will not be any closer to the aurochs on an organismical basis that is recognizable in the phenotype(including not only morphology but also all other aspects of the organism). It is only my personal opinion but I am rather confident with my statement for the reasons I gave here. 

* I found nothing so far that hints how the SNPs will influence their selection scheme. So if future Tauros cattle indeed show a higher match, which would surprise me, it would probably be coincidence. 

I would say it would be honest and fact-based if you do not claim that you execute breeding-back  on a genetic level unless you: 
- have identified the loci responsible for the organismic differences between aurochs and domestic cattle
- have identified the individual wildtype alleles on these loci and have traced them down in modern cattle 
- have collected a set of cattle breeds that evidently contains those wildtype alleles in sufficient quantities 
- breed on a genotypic and not phenotypic basis by screening the genome of each individual and select in a way that more progressed generations contain a higher number of wildtype alleles than the parental generation

Unless you do not do that, I would say that you do not “breed-back” on a genetic level. Thus, what has been presented so far does not really work for “genetic breeding-back” in any way that is relevant. But it does work as a fig-leaf in press releases to back-up the statement that you work on a genetic level and to give the whole a scientific touch. It apparently works well, as the claim that “Pajuna is genetically closest to the aurochs” is already quite widespread in the internet.*  

* I am not saying that Pajuna is not aurochs-like, far from it, I am just saying that the work that has been done does not sufficiently endorse this statement. 

What can be expected from current projects then?
If no current project is doing a true selection on the key genes of the aurochs, which are not even identified yet let alone located in living cattle and possibly a large number of them is not retained in domestic cattle anyway, what can we expect from “breeding-back” then? Actually, the same as we did before some projects started to include “genetics” in their public relations in 2009: a population of robust cattle that shares a number of aurochs-like traits in external features (such as body shape, coat colour, horns, size etc.) that is also hardy and robust at the same time so that it fulfils the ecological niche of the aurochs in its natural environment but still they will remain domestic animals which will be recognizable in traits shared by all domestic cattle on this world (reduced brain volume and sexual dimorphism, modified morphology and altered developmental biology et cetera). Basically, they will be bovine Tamaskans (what that is supposed to mean will be explained in a future post) but they will do the ecological job sufficiently and look/work authentic at the same time. Which is actually pretty much and a desirable goal which I am looking forward to. 

This will not be the last post analysing the differences between aurochs and cattle on an organismic basis. I am planning to do some more and they are in preparation. 


1Orlando, L.: The first aurochs genome reveals the breeding history of British and European cattle. 2015. 
1Visscher, P.: Sizing up human height variation. Nature publishing Group. 2008.
2Kemper, K., Visscher, P., Goddard, M.: Genetic architecture of body size in mammals. Genome Biology. 2012.
3Bollongino et al.: Modern taurine cattle descended from small number of near-eastern founders. 2012. 
4Dominic Wright: The genetic architecture of domestication in animals. 2015. 
5Dobney & Larson: Genetics and animal domestication: new windows on an elusive process. 2006. 
6Schubert et al. 2014: Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Sunday, 21 October 2018

The real differences between aurochs and cattle

This is another post that might be rather theoretic and goes pretty deep into genetics and other aspects. What I am trying to do here is to give “breeding-back” a scientific backbone. I am not a scientist of course, but my attempt is to go in-depth with the help of the knowledge that I gained in four years of studying biology at the University of Vienna and all the intense literature research I did and discussions and conversations I partook since I started being interested in “breeding-back” in 2011. And actually I think that I gathered a lot of verifiable information in these years. 

Now with this article I am trying to really go deeply into a very important basic matter of “breeding-back”: the differences between aurochs and cattle on a complete, organismic level. It shows that these differences go far beyond differences in horn shape or body size but concern nearly all biological aspects of these animals. This is, in my opinion, very important as it helps to understand what the aurochs, domestic cattle and “breeding-back” results really are. 
This is a subject that I have already covered partly these posts: 
If you feel you are new to this subject, I suggest to have a quick read through these posts. Now it is my aim to write one big, comprehensive synthesis that clearly underlines the wide-ranging differences between aurochs and cattle. 

What is very interesting, and you will hopefully see that very clearly, that all aspects of a living organism are interconnected. Developmental delays or extensions grossly affect the morphology of an animal, which is itself influenced by endocrinology. Endocrinology also affects neurology, which itself affects behaviour. It is not only that factors influence other factors directly via cascades, but some aspects are also connected because they are regulated by the same genes that influence more than one trait. For example, the same genes that affect neurology and behaviour also influence colouration. This phenomenon is called pleiotropy. A living organism is one functional entity. You cannot alter one factor without altering one or several others. This is what happened during domestication and the whole organism has been altered and modified – and not only its morphology and behaviour. And all of these factors are laid down in the genome (except for some aspects that might be influenced by epigenetics, but these are of minor importance here). 

The problem now is that we do not have the wildtype, the aurochs, left alive to study and directly compare to domestic cattle. Only morphological aspects and some of its behaviour are known with certainty, as much as the genome of one individual [15]. The fact that one genome has been resolved only means that we know the sequence of its nucleotids, not that we know the individual role of each single gene in the complex interplay that shapes an organism such as the aurochs. Therefore, to access the differences between aurochs and cattle on organismic basis, we have to take other domestic animals and their respective wildtypes as a comparison. Luckily, domestication seems to work by the same mechanisms and rules in all species that have been domesticated so far [1,2], and some of them, such as the Yak, are more or less closely related and serve as a useful analogue. Thus, we can use these species as a model for the organismic changes from wild to domestic and apply them to aurochs and cattle. 

What is domestication from an evolutionary selective perspective?

Before we go into the organismic that result from domestication, I want to outline what domestication does from an evolutional. In domestication, basically a more or less small population of wild animals is snatched out from the wild and opposed it to relaxed selection on the one hand and massive directive selective pressure on the other hand. The animals are in human custody and therefore less exposed to weather and predation, seasons, are supplied with sufficient amounts of food all year round and the food includes a smaller spectrum than in the wild, they do not have to prey for themselves (in the case of predatory species) and they also have medical care (to a certain degree and not that much in prior millennia). Thus, the requirements on the physiology of the animals (acuteness of senses, endurance, strength, food, robustness, hardiness) are much lower than in the wild. To a certain degree, due to raising animals by hand and the logistics of handling domestic animals, social and parental instincts also become less important and seasonal adaptions loose meaning as well. Another very important aspect is that domestic animals experience far less intraspecific selection as breeding is controlled by humans. There is, mostly, no concurrence between the individuals for breeding success, no sexual selection via female choice or competition, and it is not necessarily the case that the most dominant or most socially competent individuals have the highest number of offspring. Intraspecific selection is a very important evolutionary factor that is lacking almost completely in domestic animals. 
This is where relaxed selection slowly reduces these traits or at least allows these traits to become reduced. Directive selection is, however, actively executed by humans. They bred for certain morphologic and behavioural traits including economic value (milk, meat et cetera), tameness, trainability, and also aesthetics and whatever else requirements human farmers had and have on their animals. New alleles appear as mutations, some of which are considered advantageous by the breeders and become fixated in the population, eliminating their wildtype pendants. Furthermore, genetic drift and the founder effect play a role as well when the population is created and then spread and increased in number, causing a more or less coincidental distribution and disappearance of alleles.
Both relaxed selection and conscious active directive selection as well as genetic drift acted upon domestic animals over millennia and produced animals that differ from their wildtype in looks and behaviour but basically all aspects of the organism (genomic, developmental, neurological, morphological, behavioural, ecological to a certain degree), which is why I write of the organismicdifferences between wildtype and domestic. 

The Domestication syndrome 

The “domestication syndrome” describes the fact that domestication obviously affects all mammals in a similar way with the same organismic changes. These concern, for once, morphology: all domestic mammals show paedomorphy (retention of juvenile characters) in morphology, changes in size, reduction of sexual dimorphism, often hanging ears or modified appendages (changes in horn shape/size and count if present, skin flaps or enlargement of already present appendages), changes in proportion and modifications of coat and coat colour[2,3]. Furthermore, they all have the same behavioural changes which they have primarily been selected for, manifesting in reduced fear response and behavioural paedomorphy (f.e. tail wagging in dogs), agreeableness and trainability2. Domestic animals also all show similar affections of physiological traits and the same reduction of fitness of the genome called the “costs of domestication”[4, 5]. What is also very typical is a loss of seasonal adaptions. Domestic animals tend to mate and reproduce all year round, including cattle, while the reproduction circle of wild animals is adapted to the seasons of the year2

Cattle are a perfect example of the domestication syndrome, at least for traits were we can directly compare them to their wildtype (that is mainly morphology and to some degree behaviour). For all the other aspects, other domestic animals serve as a models for other organismic differences that we can predict with high certainty because it apparently works the same in all domestic mammals. I am going to break down these differences point by point. 

Morphological changes in domestic cattle 

The morphological differences between aurochs and cattle are obvious and have been covered multiple times on this blog (a quick look at the Wikipedia article might teach you the most important facts). In fact, all of these differences are classic “symptoms” of the domestication syndrome: shortened legs and an elongated trunk, in most cases decreased and in some increased body size, reduced sexual dimorphism in body size and colour, reduced skull size and brain volume and paedomorphy in skull shape (shortened face, especially the snout, larger eyes and concave profile in many breeds). Also the "hump" created by the elongated processus spinosi in the shoulder area that is characteristic for the aurochs and other wild bovines, is reduced or completely absent in most breeds. According to the literature, the aurochs skeleton was more robust [6], indicating that the aurochs was more muscular than domestic cattle. The horns have mostly decreased, in some cases increased, in size and developed a lot of different shapes, often loosing the inwards-curve which is typical for horned domestic animals[7]. Some breeds, mostly zebuine, have hanging and/or enlarged ears, skin flaps such as the dewlap, the scrotum and the udder is enlarged in most breeds. The fur sometimes is shorter and not as insulating as to be expected in a wild animal, some breeds, such as highland, have long hair all year round and lack the bilayered fur. Some have curly hair all over the body, some completely lost curly hair. Whether or not hair is curled is regulated by specific genes. A lot of colour mutations evolved, including those causing the typical domestic piebald colour. 
Domestic cattle often have elongated appendages (skin flaps like the dewlap, elongated scrotum). I have been puzzling around what might be the cause of that and I was not able to come up with a developmental, hormonal or neurological connection so I speculate that it might caused by specific genes, perhaps such involving connective tissue formation. In wrinkled dogs, a gene involved in the production of hyaluronic acid synthase 2 causes wrinkling of the skin (also in humans) [14]. 

Affections of development in cattle 

How an organism is going to take shape is determined by when and how much of specific genes is going to be produced, and when they stop. You can produce different morphologies with the same genetic programme via a developmental delay or extension. Domestication usually causes a developmental delay, what means that development stops earlier than in the wildtype. The result is paedomorphy, which is universal among domestic mammals. It is possible that a selection for reduced tameness caused paedomorphy in behaviour (reduced fear response, agreeableness) and by pleiotropic effects and developmental cascades also a paedomorphic morphology. In a sense, domestic cattle are paedomorphic aurochs. In castrated individuals, steers, the removal of the gonads extends some of the developmental pathways as the stopping signal of the gonads is off, and therefore some of the paedomorphic traits are compensated. Steers may have a somewhat more aurochs-like morphology regarding size and proportions – they are more long-legged, long-snouted and also the horns grow longer (some examples here and here). An example for the influence of developmental delay/extension that I investigated myself is horn curvature. I took the Taurus bull Latino’s skull and pushed the rather banana-shaped horn sheaths outwards to the tip of the horn bone, following the curvature – suddenly there was a perfectly aurochs-like horn curvature, the “primigenius spiral” and also the size was right (see here for a sketch). If the horns would have continued to grow significantly (note that the bull was mature) horn curvature and dimensions would have matched those of the aurochs. Thus we can speculate that the actual genes regulating these traits are not different in Latino from those in the aurochs, only the development of the horns stopped earlier in this domestic individual (this, of course, also has consequences for breeding but those will be covered in another post). In the case of drastically deviant horn shapes (such as this one), there might indeed be mutations involving horn curvature. The skull anatomy of cattle is also a classic example for paedomorphy and thus developmental delay. In breeds with a very pronounced paedomorphic skull, the snout is shortened and concave, the nose is rounded and the eyes are enlarged. Actually, in most cattle breeds both the snout and frontal area is shortened (the latter might also be related to horn size), and also the eye sockets of bulls are not as prominent as in aurochs as far as I can tell from domestic bull skulls I have seen to far. I like to call this a “calf face” and developmental delay is very likely to be the cause for these traits. Maybe in extreme examples, such as the bulldog faces of breeds like Cachena and Barrosa, special mutations might be responsible for the condition we see, just the short legs in dachshunds[8], but in most domestic cattle the skull shape might merely be the result of development. 
Most domestic animals, as a result of the developmental delay, also reach sexual maturity faster than their wild counterparts. Domestic cattle are sexually mature about one year faster than extant wild bovines. 
The timing and extent of gene production plays a crucial role, or the crucial role, how an organism is going to develop and it is very likely that extensions or delays, most likely delays, of gene production as a result of selection on tameness has produced a lot of the morphological changes typical of domestic cattle compared to aurochs without necessarily involving extra mutations of the genes that actually regulate the respective body parts (see the horn example). Responsible for developmental delays and extensions are transcription factors that regulate gene activity, which are itself regulated by regulation genes and signal molecules (hormones) produced by the glands of endocrinologic system (these are, again, itself regulated by genes as well). It seems that selection on tameness alone caused a number of drastic changes in the organism in each domestic species that must be laid down in the genome [2], and so in cattle. 

Endocrinologic changes and their consequences 

Two hormone classes seem to play an important role in the domestication of mammals. One of them are corticosteroids which are involved in stress reaction. Domestic animals have a reduced fight/flight reaction, and indeed the corticosteroid level in domesticated foxes dropped by one quarter compared to the control group [2], indicating a causal relationship. We can assume that this similar in other mammal species as well because the types of hormones all have similar effects in mammal physiology, so probably the corticosteroid level of domestic cattle is reduced compared to the aurochs. In breeds with an inherited exaggerated fight/flight reaction, such as the Spanish fighting bull, it might be higher compared to the average of domestic breeds. Doing research on google I discovered something that fascinated me that might be of high relevance: the cushing syndrome in dogs. More precisely, it is called hyperadrenocorticism and describes an over-production of cortisol by the pituitary gland (see here). The symptoms are, among others, lethargy and a morphology that is remarkably similar to domestic cattle: enlarged belly size, reduced muscling, hanging spine (see here and here).   
Another very important class of hormones involved in domestication are thyroid hormones. These hormones have a great impact on the development of many morphological, physiological and also behavioural traits [3]. Thyroid hormones are involved in growth, stress response behaviour, hair growth, adrenal and gonad gland function and pigmentation. Hypothyroidic rats are smaller than normal ones and possess floppy ears [3]. Domestic rats have a smaller thyroid gland than wildtype ones, which is probably linked to increased tameness [3]. Neoteny in amphibians is caused by thyroid hormones as well, and disorders of thyroid hormones cause cretinism in humans. The symptoms of cretinism are shortened extremities, reduced body size and lowered cognitive abilities. This is remarkably similar to what we see in domestic animals. Considering that thyroid hormones are involved in hair production and pigmentation, I think Matthias Scharf’s (from the ABU) suspicion that cattle which have this colour variant that also goes hand in hand with brittle horns and hair have some metabolic or hormonal disorder is perfectly plausible. 

Looking at the effects of both corticosteroids and thyroid hormones on behaviour and morphology, actually I think that we have found the key here, my friends. It seems that selection on behavioural aspects, mainly tameness, changed the hormone system in a way that the aurochs’ skeletal proportions and morphology was changed to what we see in domestic cattle: shortened limbs, reduced size, reduced brain volume and skull size, less muscling and enlarged belly, occasionally a hanging spine. This is perfectly in line with the evidence we get from other animals. 

Neurology and morphology 

The behaviour of animals is not only influenced by the endocrinologic system but of course also the nervous system. Thus, neurological development and neurological genes probably also were altered in selection. These, however, do not only affect behaviour but have a deep impact on the rest of the body. The neural crest is a precursor of many tissue types, influencing f.e. the adrenal gland and pigmentation [1]. For example, melanoblasts (the precursor cells of melanocytes which are responsible for pigmentation) develop in the neural crest and migrate in the target tissue (skin, hair et cetera). Certain alleles on the KIT  locus (called “Star” by Belyaev) cause a delay in this migration during which these cells die, resulting in unpigmented areas in the face (in homozygous foxes at least also body) that we see in most domestic mammals, including cattle (even in humans, where it is called “piebaldism”)[3]. Many of the “colour genes” are actually multifunctional genes that also have a metabolic or neurologic function. For example, mutations of the Dunlocus can cause neuromuscular disorders, such as rolled tails in dogs and pigs caused by myelin degeneration [9]. The Agoutilocus also plays a role in regulation of fat metabolism in the adipocytes[10]. 

Loss of physiological fitness 

Not much is known about the physiology of the aurochs, as there are no living aurochs to study, unfortunately. But there is a comparably close relative of the aurochs that has been domesticated and is still extant in both its wild and domestic form: the yak. This makes it a useful model for the physiological changes that domestic cattle might have undergone during domestication. The differences between wild yak and domestic yak in physiology are considerable. For example, the proportions of g-globin to total globin is higher in the wild yak than in domestic yaks, probably linked to higher stress resistance. Wild yaks also have a higher endurance as the activity of lactate dehydrogenase which prevents muscle fatique is higher in the wild yak. The respiratory metabolism of the wild yak is probably also more efficient as liver, lung, kidney and heart consume less oxygen and the quantity, size and bulk of red blood cells is higher. The wild yak might also be more efficient in digestion as the content of free amino acid in the serum is four times higher than in the domestic yak, and wild yaks keep on increasing in weight during winter, whereas domestic yaks decrease (domestic cattle do so as well) [11]. The death rate in winter is 4% lower in the Datong yak (which is a hybrid breed of domestic and wild yak) [12], so it might be even lower in wild yaks. Wild yaks also have a higher quantity and quality of ejaculate. I think that the physiological differences between aurochs and cattle must be of a very similar manner. The yak was apparently domesticated 4500 years ago [13], and therefore its domestic history is only half as long as in domestic cattle, and basically all of them are landraces and thus not as protected from abiotic and biotic factors as more derived cattle breeds. Therefore I actually expect the physiological differences between aurochs and cattle to be more intense than between wild and domestic yak, at least in the more derived cattle. In pigs domestication also influenced leukocyte count, growth traits, meat character and disease resistance [1], so these factors might also be affected in cattle. In horses, domestication apparently also affected skeletal muscle performance, joints and skeletal articulation, balance, locomotion and the cardiac system [5]. Surely each of these changes reflects the purposes the species was domesticated for, and horses were primarily selected on work purposes. But at least some of these aspects might be affected in domestic cattle as well, especially because the domestic life does not have the same physical requirements as living in the wild as an aurochs. Last but not least, and this is the only case where we have direct evidence from the aurochs genome we have, genes for milk production and quality have been altered by selection [15]. 

Loss of genetic fitness

It is not known whether aurochs and cattle differed in karyotype, or if cattle experienced genomic mutations such as duplications or deletions of entire genes. But what we can say with certainty that the genome must have “suffered” from domestication in a similar manner as in all domestic animals. This includes a loss of genetic diversity and therefore an increase in homozygosity due to the founder effect, genetic drift and numerous bottlenecks [4]. The absence of purifying selection for evolutionary fit traits plus new mutations probably led to an increase of deleterious alleles in the cattle genome (mutation accumulation), because this is what we find in other domesticated organisms [1,4]. This phenomenon is described as the genetic costs of domestication and the deleterious alleles can affect all possible aspects of the organism, including morphology, growth, disease resistance, metabolism, reproduction, neurology and many others [1,4,5]. Conscious inbreeding, especially in the latest two centuries, further intensified the loss of genetic fitness of domestic cattle. This process is still on-going, especially since the more derived breeds are becoming an increasingly important part of the domestic cattle gene pool and absorbing the less derived landraces all over the world. 

Summary.It occurs that there is a long way from an aurochs to modern cattle on organismic basis, despite both being assigned to the same biological species.  Apparently selection on tameness and other characters drastically affected the timing and amount of development of the organism. Developmental delays and alterations of endocrinology such as the corticosteroid and thyroid hormones as a result of selection on behaviour changed the morphology of the aurochs dramatically and produced a phenotype with (mostly) smaller size, shorter legs, paedomorphic skull with reduced brain volume, reduced sexual dimorphism, enlarged belly, reduced muscling and altered horn shape and size. Selection on behaviour also influenced the neural crest development, resulting in affected pigmentation showing in unpigmented areas (piebaldism) in many breeds. Additionally to that, new colour mutations evolved, which might also affect metabolism and neurology. For a number of extreme phenotypes, such as stubby legs and faces, additional new morphological mutations might be responsible. Modifications in behaviour made domestic cattle much more tame, agreeable, trainable and lethargic compared to the aurochs – these changes correlate with the morphological traits because of genetic and hormonal interconnections. As a result of relaxed selection, not only the seasonal adaptions but also the physiological fitness of domestic cattle must have reduced significantly, probably concerning metabolism, digestion, respiration, endurance and stress resistance, which would very likely impact the survival rate under natural conditions as in the case of the yak. From a population genetic/evolutionary perspective, domestication probably reduced the genetic diversity and fitness of the population as a whole compared to the wildtype, which is typical for domestic animals. 
All these changes in sum comprehensively concern the whole organism of the animal. Despite being assigned to the same species and being able to reproduce readily with each other, aurochs and cattle are two completely different types of organisms – wild and domestic. Surely the extent of these differences will vary between breeds, especially between less-derived landraces such as Maronesa or Turano-Mongolian breeds and highly-derived breeds such as the Holstein-Frisian and others, but the differences outlined in this article are very basic and must be universal among domestic cattle as they simply describe the state of being domesticated. I expect variation among breeds only to concern the extentof these changes, not whether the total of these changes is there or not. Furthermore, while it is true that some cattle might be closer to the aurochs than others, I consider it more than likely that all modern domestic cattle are closer to each other than to the aurochs, and that the distance to wild aurochs is quite considerable even in a less-derived breed like Maronesa. 

Consequences for breeding-back 

I think that diagnosing those wide-ranging differences between a wild animal and its domestic counterpart, especially between the aurochs and domestic cattle, has highly relevant implications for the understanding of what “breeding-back” results are. Actually, having researched these dramatic differences that thoroughly makes “the aurochs was larger, had a specific colour and different horns” rapidly loose meaning and almost sound like Kindergarden stuff to me. And judging on a total organismic level it actually it is, in a sense. When I started being interested in the aurochs and “breeding-back” in spring 2011, I looked at wonderfully bred individuals of the Wörth Heck cattle line such as the bull Aretto or the cow Erni and I did not quite understand why those animals should not be considered aurochs. My thought was: the phenotype matches, and the phenotype is a product of the genotype, so why not? Nowadays I am not only aware of the phenotypic differences (size, morphology, behaviour and so on) but I also understand that the differences go far beyond, affect nearly all organismic aspects of the animal and that the genotype definitely would not match in any case. I hope this becomes obvious from this post. Back in the time of the Heck brother’s experiments, for example, these differences where not even known to nearly the same extent. Apart from that, the Heck brothers overlooked many of the morphological differences between aurochs and cattle and failed to properly judge what they bred (for more details, see here). Why should one of their bulls be a resurrected aurochs? Because of similarities in colour and horn shape? From a modern perspective I would say: you cannot be serious, this is not even 2% of the story. So even if breeding manages to fix body size, proportions, horn shape, snout length and other aspects, “breeding-back” results will still remain domestic animals and therefore different animals. The interconnections between morphology, behaviour, development and all the other aspects are so complex and involve so many loci that I do not think that traditional breeding can truly reverse the changes caused by domestication. This is why I mostly write “breeding-back” under quotation marks and strongly reject the term “rebred aurochs”. 
However, some modern projects claim to execute “breeding-back” on a genetic level in order overcome these problems to achieve a more authentic result that might deserve the title “aurochs 2.0”. In the next post, I am going to present my personal take-on to the facts behind this claim. 

Most of the research for this article I did on my own, but I also have to say that some of the references, especially those on the yak physiology, I would have never discovered without the precise and thorough research work of Roberta on the Carnivora Forum Aurochs thread. It helped me great time to complete my body of theories on this subject. Many thanks for that! 


1 D. Wright: The genetic architecture of domestication in animals. 2015. 
2 L. Trut: Early canid domestication: The farm fox experiment. American Scientist. 1999.
3 K. Dobney & G. Larson: Genetics and animal domestication: new windows on an elusive process.2006
4 Moyers et al.: Genetic costs of domestication and improvement. 2017. 
5 Schubert et al.: Prehistoric genomes reveal the genetic foundation and costs of horse domestication. 2014. 
6 W. Frisch: Der Auerochs: Das Europäische Rind. 2010. 
7 Hans-Peter Uerpmann: Der Rückzüchtungs-Auerochse und sein ausgestorbenes Vorbild
8 Kemper, Visscher & Goddard: Genetic architecture of body size in mammals. 2012. 
11 Zhonglin: Development of a new yak breed through utilization of wild yak genetic resource – serial technologies of the development of the Datong yak breed.2004. 
12 Lanzhou Institute of husbandry and pharmaceutical sciences: The 5thinternational conference on yak. 2015. 
13 Lensch, Schley, Zhang: Der Yak (Bos grunniensis) in Zentralasien. 1996. 
15 Orlando, L: First aurochs genome reveals the breeding history of British and European cattle. 2015. 

Thursday, 18 October 2018

Teaser 2

Actually I don't want to post two teasers in a row but the two posts I have in preparation delay a little bit because of the effort I put in it. They should be comprehensive and well-researched. And I decided to switch the sequence. At first I want to post one on

- The organismic differences between aurochs and cattle: A complete comprehensive coverage of all the differences in morphology, physiology, development and genomics that must have been there to deeper understand the different nature of aurochs and cattle and wild and domestic. 

after that, it seems logical to cover 

- Genetics in breeding-back, whether or not genetic breeding-back is possible and if any of the current projects are doing it. 

After that, I want to cover a special dog breed named Tamaskan and its meaning for breeding-back. Also, I want to do a short post on the evolution taking place in Oostvaardersplassen. And, something I did some months ago and want to finally present to the public is 

- A volumetric weight calculation for a male aurochs based on a model. 

Furthermore, I want to self-interview me in a post on some all possible aspects of breeding-back that have been covered on my blog so far. 

And after having done all that, I want to do one comprehensive and handy overview over all the long and important posts I did during the last five years of blogging on breeding-back. 

As you see, I am incredible motivated at the moment and I hope you stay tuned! 

Tuesday, 9 October 2018

Picture of the day: Indian aurochs with hump

I am going to start with doing pictures of the day, considering that I have so much material but so little time to put them into practice properly. So for now, a picture of the day. 

A while ago I did another post on the Indian aurochs, Bos primigenius namadicus. It also includes a new life restoration. In the post, I go over my anatomical speculations point by point. I have not yet considered the fleshy zebuine hump a probable wildtype trait of the Indian aurochs subspecies because it was not possible to identify any functional purpose for the hump (which is, in fact, a hypertrophied Musculus rhomboideus) in the literature yet. So I did not consider it a probable wildtype trait as it is apparently unfunctional. However, one of my readers pointed out to me that it might have display function. 
This idea is actually not that implausible. First off, Bantengs and Gaurs both rely more on display than combat fight than cattle do and as a consequence, they have a shorter and higher profile with high processus spinosi that are not muscled all the way up as in cattle. Also, their horns are more upright instead of fowards-facing as in the wildtype of cattle, the aurochs. Now the Indian aurochs has proportionally way larger and more wide-ranging horns than the European subspecies, which I suspect are less functional than smaller and more compact horns in combat. This might be a hint that the Indian aurochs relied slightly more on display than the European one. The zebuine hump definitely increases the height of the profile of the animal, as do the elongated processus spinosi in Banteng and Gaur. So perhaps the zebuine hump might indeed qualify as a possible wildtype trait, although this is pure speculation. 
And I could not hesitate to illustrate this idea: 
Most likely only contemporaneous art might resolve the question whether the Indian aurochs had this trait or not. 

I feel that my interest in the Indian clade of the aurochs and in zebuine cattle is increasing. Actually I plan to do more research on zebuine cattle, and maybe also do a zebu series on my blog. Lots of research to do, and so little time alas, so please stay tuned. 

Friday, 5 October 2018

Teaser: genetics and breeding back

At the moment I am extremely busy but also extremely motivated to write some more in-depth posts. I have two blogposts in preparation: 

- one covering theoretical assumptions on aurochs genes present in living cattle plus what current breeding-back projects are doing in this respect
- one covering the organismic differences between aurochs and cattle that must be there based on comparisons with other domesticated species 

I think both posts would cover some important aspects that should be discussed in the modern breeding-back world. 

I can't promise when I am done with the posts, probably during the following weeks or so. Please stay tuned!