Sunday, 1 December 2019

Breeding works with coincidence

When two individuals of different genotypes are crossed, it is not that important what the F1 looks like, as it represents maximum heterozygosity that is possible between two breeds. On each locus, it will have one allele from breed A and one from breed B while the goal of targeted breeding is the opposite, it wants to unite the desired traits of A and B on each locus homozygous, therefore, to stabilize the desired characteristics of the parental breeds in the new line. Therefore, the looks of an F1 are not actually all that relevant. In second-generation crosses, it becomes more complicated. Genes (or actually: chromosomes) get passed on entirely by coincidence, therefore there are numerous possibilities what a true F2 will look like, with a pure individual of breed A or B being the ends of the extremes. At this very early stage of crossbreeding, it would be a quite big coincidence if two F2 would happen to look exactly the same. I have an example from the Lippeaue here: 
 
Lale (Heck x Sayaguesa) x (Heck x Chianina)
Latina (Heck x Sayaguesa) x (Heck x Chianina) © Matthias Scharf
Both cows are (Sayaguesa x Heck) x (Chianina x Heck), yet they look very different. Lale has comparably long horn, a Heck cattle-like appearance overall except for the head, plus a slightly diluted coat colour. Latina, on the other hand, has the long-legged stature of Chianina and also the head and very small horns resemble Chianina. It has no phenotypically visible dilution in its coat colour. The likelihood for each trait was 1/4 for Sayaguesa or Chianina traits and 1/2 for Heck traits. 
There is also a (Sayaguesa x Heck) x (Grey cattle x Watussi) bull called Rimu in Hortobagy. It turned out quite nice as you see on the photos. It was a lucky coincidence that it looks this way, it could have also gotten the semi-dominant dilution of Steppe cattle, the short face of Heck cattle or upright horns. The likelihood would have been 1/4 for each of the traits of the founding breeds. 

So when I write “Sayaguesa and Chianina is a good combination” (f.e. here), I do not mean that I believe that F2 will perfectly unite the good traits of the founding individuals in one, but simply that they have the potential to do so. A F2 Chianina x Sayaguesa might either have a perfect aurochs colour, good horns, long faces, long legs and large size (the maximum potential for aurochs-likeness that is in this combination), or it might end up completely white or at least diluted, having tiny horns and being not as large and long-legged as Chianina (so none of the desired traits of the founding breeds united in one individual) – most individuals will end up somewhere in between. F2 will show the full spectrum of all possible phenotypes, no matter which breeds are involved. You can say the same of all possible genotypes as long as you are not crossing or backcrossing with purebred individuals (basically, the un-stable inheritance of Heck cattle, which have a heterogeneous genotype, represents the same phenomenon).  

Thus, breeding is simply a numbers game, you need either luck or you have the produce large quantities of the combinations and select the best out. As cattle unfortunately have the small litter size of only 1, perfect breeding takes a while.


Thursday, 28 November 2019

An overview over the F1 Auerrind cattle

The website of the Auerrind project just posted an overview over the F1 Auerrind crosses so far. It is very nice to see them all in a row, and as recently announced, the first second generation crosses of the project are under way as well. As Claus Kropp correctly writes, it is not that important what the F1 look like but what genetic potential they have. Nevertheless I want to shortly describe the F1 here in this post. 

The Auerrind project has five Sayaguesa x Chianina so far. The cows are noticeably lighter in colour than the bulls. The bulls have slight greyish tone because Chianina has a semi-dominant dilution allele that removes the black pigment, additionally to recessive dilution alleles that remove the red pigment. Therefore, F2 Sayaguesa x Chianina have a chance of 1:4 for having the phenotypically right colour, 1:2 for looking the same as the F1, and 1:4 for being completely diluted concerning this allele. That's not so dramatic for breeding, as colour is the easiest to breed for. I like the body shape of the older F1 bull, it seems to develop quite good. 

In the Sayaguesa x Grey cattle crosses you see that the cow is much lighter in colour than the bull. The colour of the cow is slightly diluted, while the bull is completely black. All in all, the bull looks a bit like an aurochs-coloured Grey cattle bull to me, it is interesting that the Grey cattle influence is that strongly visible in this individual, whereas you see the Sayaguesa influence in the Sayaguesa x Maremmana very clearly. Good breeding partners for both combinations might be Sayaguesa x Chianina, which would have the potential for good size, body shape, horn shape and skull shape, whereas there is a chance that they would have some greyish dilution in the fur colour.

The Maremmana x Watussi look interesting as well. The colour of the cow is very beautiful. Hard to say what would be the ideal breeding combination for these two, perhaps Sayaguesa x Chianina or something 3/4 Sayaguesa. 

There also is another photo of Alvarez, the Sayaguesa x Watussi bull. It seems to grow very impressive horns that also face forward, and its face is rather Sayaguesa-like. The colour is perfect. As I wrote in another post, I think Sayaguesa x Chianina would be the perfect combination for this guy, and such crosses are about to be produced soon. 

It also has a photo of the first Chianina x Watussi individual. It is a cow, and the colour is very reminiscent of that of the Sayaguesa x Chianina cows. It will be very interesting to see how large its body size and horn size will be, since it is a mix of a large but small-horned and a small but large-horned breed. If bred to a Sayaguesa bull, the results could be pretty similar to the Sayaguesa x (Heck x Chianina) individuals from the Taurus cattle, which turned out to be a very successful combination, perhaps with even larger horns. Another option would be Sayaguesa x Chianina (this combination is good in almost each combination as it has a lot of the important traits except for horns size). 


Sunday, 24 November 2019

New photo of Alvarez the Auerrind bull

The Sayaguesa x Watussi bull is now subadult and Claus Kropp presented a recent photo:
© Auerrindprojekt
As you see, it has a flawless colour, the horns seem to start to curve forwards and not as upwards as in Watussi, and the body shape is a bit better than in Watussi. It is as large or a little larger than its father and still growing. It will be very interesting what the final horn shape and size is going to be. 

Maybe the ideal breeding partner for this bull is Sayaguesa x Chianina (the bull will be moved to the herd with the cows of this combination soon). It is, of course, playing with luck how good the second-generation individual will look like. Alvarez might either pass on either the flawless colour, Sayaguesa-type body and large horns, or Watussi traits and Sayaguesa-type horn size et cetera, while the Sayaguesa x Chianina might either pass on the right colour or dilutions, small horns or the right horn curvature and colour and so on. Breeding works with luck. 
One method to reduce the amount of luck necessary would be to produce good F2 of the respective generations first. An F2 for Sayaguesa x Watussi should have many Sayaguesa traits but have large and thick horns, a F2 for Sayaguesa x China should have the right colour, right horn shape and be large, long-legged and slender. F2 would also be more stable on these traits than F1, which are not stable at all for genetic reasons. These good F2 could then be bred to each other in order to seize the maximum potential in this combination. This would, however, add one additional generation to the breeding, but I think it would be worth the effort. 

Anyway, a (Sayaguesa x Chianina) x (Sayaguesa x Watussi) has a high potential for uniting many aurochs traits, and if a sufficient number of individuals of this combination is produced, some might look superb. 

Friday, 15 November 2019

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. 


Monday, 11 November 2019

The Cuxhavener Küstenheiden

The Cuxhavener Küstenheiden in Niedersachsen,Germany, is a Taurus cattle breeding site that has not been covered here in the past, but has some really good animals. They started about 15 years ago with 24 animals, two of them being the cow Lusitania and the bull Lehmann. Both were Sayaguesa x Heck and both were from the Lippeaue. Lehman was used as a breeding bull until recently and was rather slender with long legs. 
You can see the herd in these three videos: 

Video 1 Here you can see Lehmann at 1:48, and 3:35, just see the good body shape of both individuals

In the third video you see them being handled from 34:00 onwards. I think those are very beautiful shots. The colour of the herd is comparably uniform, the horn shapes are OK to very good, and most of the individuals are slender and long-legged. Their colour and their coat that starts to turn into a winter coat are especially beautiful in these foggy autumn shots, with the forest and the grassland in the background. It looks very natural, you can easily believe that these animals are indeed autochthonous wild game also because of their almost uniform appearance. Here you see some more individuals from the herd. Some cows have small white spots on the belly, but the extraordinary slenderness of many of the individuals, the cows in particular, compensates that in any case. 

I would say that right after the Lippeaue, the Cuxhavener Küstenheide is the second-best Taurus cattle breeding site in Germany. 

Friday, 8 November 2019

A Chianina-Sayaguesa breed?

Claus Kropp recently sent me a video of the Chianina cows and one of the Sayaguesa bulls of the Auerrind project running next to each other which was pretty impressive. Not only have the Chianina cows a very useful horn curvature, but also was the bull noticeably larger than the cows, which have a withers height of 165cm. This in turn must mean that the bull is at least 170cm tall. Both are tall and slender breeds; Chianina is larger on average and has a good horn shape, Sayaguesa has the right colour and larger horns but is not always that long-legged as Chianina, and so far all Chianina x Sayaguesa crosses looked good. So I had the idea: why not making a breed that is a mix of exclusively Chianina and Sayaguesa? If well-selected such a herd would have the perfect colour, horns with a very good curvature (albeit not very large) and excellent body size and morphology with long slender faces after a couple of generations. Such a strain would be of great use for any project, be it Tauros, Taurus or the Auerrind project itself. 
What is missing in a Chianina-Sayaguesa mix is a breed that adds the long and thick winter coat, as the winter coat of Chianina is not very long and dense and that of Sayaguesa is not as good as that of f.e. Heck cattle either, additional to the small horn size. A Maremmana x Watussi that would be cautiously bred into the herd might fix that in one shot. The Auerrind project currently has a bull of that combination of which they do not know yet what to breed it to, I would suggest to breed it to some good F2 Sayaguesa x Chianina individuals. 
 
A Chianina x Sayaguesa bull born in the Lippeaue (© Matthias Scharf)

Wednesday, 6 November 2019

Heck bull with Watussi traits in Baden-Württemberg

The video down below shows a Heck bull which undoubtedly shows traits inherited from Watussi, see here: 

https://www.youtube.com/watch?v=aNYVJh27cW8

The video is from a grazing project near the river Sechta in Baden-Württemberg, Germany. You can clearly see the Watussi influence in its horns, the body shape, and fur. Some Heck cattle breeders deny the influence from Watussi in Heck cattle and claim that the individual marked with "Watussi" was just a Heck bull named "Watussi", but with individuals like the bull above it is impossible to deny the Watussi ancestry of large-horned Heck cattle. 

I am pretty sure that the cow at 2:12 is Loxia, a Sayaguesa x (Heck x Chianina) cow from the Lippeaue. That means this herd has both very large-horned Heck cattle as much as a good Taurus individual, what means that there is potential for very interesting offspring. 

Tuesday, 5 November 2019

Video of very interesting Heck bulls

Recently I found a video of two very interesting Heck bulls on youtube: 

https://www.youtube.com/watch?v=P944XCc6RV4

The horns of those critters are astonishing, especially those of the bull at 0:50. Unfortunately the video gives no information on where it was shot, and has comments disabled. But not only the horns but also the body shape (sloping back, sloping pelvis) and the looks of the face makes it very likely that those bulls have Watussi ancestry. Furthermore, the shoulder hump and the solid black colour reveals influence of Taurus/Sayaguesa, which makes it very likely that they are Hungarian Taurus cattle and that the video shows one of the young bull groups of Hortobagy. 
Not only are they very interesting to look at but they also give a foretaste for what the Watussi crosses of the Auerrind project are going to look like. 

Sunday, 3 November 2019

New videos from the Lippeaue

I just found some recent or more or less recent videos taken in the Lippeaue that I want to share here: 

https://www.youtube.com/watch?v=D5_PON_dUFs
https://www.youtube.com/watch?v=OYPmHzeQog0
https://www.youtube.com/watch?v=mM6fG8Im1KE
The videos shows one of the new breeding bulls (I think at Klostermersch-Nord but I'm not sure), which is half Sayaguesa and half a third generation cross if I am remembering correctly. I think it is an extremely beautiful individual. 

https://www.youtube.com/watch?v=2JtSs7GdW5c
Aerial shots from Klostermersch-Süd with Larissa and other cows with a new breeding bull. Just look at how slender and athletic the cows look and move. Larissa is the greyish-coloured cow right at the beginning, she is the biggest cow in the herd with at least 160cm, the young breeding bull is noticeably larger. If the colouring of the individuals was a little more uniform, one could easily believe aurochs are back on this shot. 

I think the Lippeaue really represents the top level of modern breeding-back. I feel like I have to visit the herds once again some time. 


Monday, 28 October 2019

Breeding-back and domestication: A summary

Last summer, I did some posts on domestication in general, the exact organismic differences between wild and domestic, between cattle and aurochs, and how this might impact the topic of “breeding-back”. The posts are the following: 


It is really a lot of content but truly relevant for the understanding of this topic and a lot of my posts, which is why I thought it would be nice to provide a little handy overview by summarizing the posts in one. 


The real differences between aurochs and cattle

All aspects of a living organism are interconnected via pleiotropic effects (when genes influence more than one trait) and developmental cascades. Hormonal activity, which is regulated by development, influences behaviour as much as morphology. Colour genes also play a role in metabolism and neurology. Not only there was massive directive selection executed upon the animals by humans, also many of the natural and sexual selective factors were eliminated by human custody. So it happens that domestication dramatically altered the whole organism in nearly every aspect: genomic, developmental, neurological, morphological, behavioural and ecological. 

Domestication affected all domesticated mammals in a very similar manner, a phenomenon which is called the domestication syndrome. Cattle are a perfect example of the domestication syndrome. The “symptoms” include reduced fight/flight reaction, increased agreeableness and docility, lethargic behaviour, reduced sexual dimorphism, paedomorphy (retention of juvenile characters, f.e. in skull shape), reduced body size, reduced limb size, reduced brain volume, elongated appendages such as skin flaps, hanging ears (in zebuine cattle), many deviant colour variants, changes in horn shape and size or loss of horns, loss of seasonal adaptions in the reproduction circle. 
The effects on developmental biology in cattle might be responsible for many of the morphological changeswe see. In particular, it was a developmental delay that causes ontogeny to stop earlier, leading to paedomorphy and probably also affecting horn size and shape (see the Latino example) as well as body size. Endocrinology (hormonal activity) might be the key for the classic domestic cattle phenotype. Especially the thyroid and corticosteroid activity might result in the reduced muscling, enlarged belly, hanging spine, shorter body size and reduced limb length and brain volume we see in domestic cattle. Since neurological genes also affect colour cells, selection on behavioural traits might have also caused the classic domestic piebald pattern. Artificial selection and a lack of natural and sexual selection probably also led to a considerable loss of physiological fitness. If the physiological differences between cattle and aurochs are comparable to what happened in yaks, domestication must have affected endurance, respiration, digestion and other factors, increasing the death rate in winter. As in horses, it might have also affected skeletal articulation, locomotion and the cardiac system. Domestication also causes a loss of genetic fitness, called the costs of domestication. Lacking selection, inbreeding and mutation accumulation leads to an increase of deleterious alleles, affecting various organismic factors. In the post From aurochs to cattle: step by step you can see a stepwise illustration of the changes from aurochs to cattle. 

Summing up all those differences made me conclude: 
these dramatic differences [...] make “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 is. 
This, in turn, means that just a similarity in horns and colour are not even a tiny bit of the whole story. 
Considering the complex interplay of all the factors concerning morphology, behaviour, endocrinology, development and the genetic base underneath it is very unlikely that traditional breeding can simply reverse domestication. This is why some modern projects now claim to execute “breeding-back” on a genetic level. A claim that will be covered in the next section. 


Is “genetic breeding-back” possible

The basic argument of “genetic breeding-back” is that no original wildtype alleles (“genes”) would have been lost during domestication but simply been split up among modern domestic cattle, and that “genetic breeding-back” aims to trace down those alleles and unite them back in one population. 
This scenario, communicated in press releases, faces two problems: 1) Are truly all aurochs alleles still present in the modern cattle population? 2) have those alleles been traced down in modern cattle? 
In order to answer the first question we have to focus exclusively on the defining key aurochs genes. Not haplotypes or other phylogenetic markers, but those genes that regulate the defining differences between aurochs and cattle described above. Considering the complexity of most of those factors, I concluded: “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“
Most important to note is that it has not been identified what those particular genes involved are. Not in the aurochs, and not in any mammal. 

The evolutionary process cattle underwent at the beginning of their domestication makes it very unlikely that all of the wildtype alleles survived this process. A very small population of aurochs was snatched out and put under massive directive selective pressure. Nowadays not all cattle are domesticated to the same extent, some are more some are less derived, but some basic organismic changes (see above) are universal to all of them, and so must be the genetic changes causing them, which makes it very likely that some of the wildtype alleles on the loci controlling these changes must have been lost completely in all strains of cattle, otherwise those changes would not be universal. The population genetic process cattle underwent during the last 8000 years – a very small population that was put under massive directive selective pressure and millennia of more or less strict reproductive isolation – leave little room for a survival of all wildtype alleles. 
Even if all the original genetic material of the aurochs was still present and split up among modern domestic cattle, the particular loci of the key genes must have been identified (which is not the case yet) and the specific alleles, wildtype and domestic, must have been identified and traced down in modern cattle (which is not the case either). Thus it is not known which breeds carry which aurochs alleles and to which extent because the necessary scientific framework has not been done yet. Consequently, as the necessary information is not there yet, no current “breeding-back” project is able to carry out breeding on a “genetic level”. Studies on phylogenetic markers and SNPs are nice but do not investigate the key genes responsible for the differences between domestic cattle and their wildtype. Therefore, “genetic breeding-back” exists only in press releases. 


Cattle are “designer aurochs” 

“Cattle and aurochs” is actually a wrong dichotomy. There is no distinctive, definite line between those two animal types as the transition from a wild bull to a Fleckvieh bull was fluent and aurochs and cattle probably hybridized without any obstacles on occasion wherever they neighboured. Actually, cattle are man-made modified designer aurochs – “cattle” is just the term we use to refer them to. Therefore, it is helpful to describe cattle simply as modified aurochs instead of creating a separate category of animal, and for my post Cattle are designer aurochs I chose individuals of three breeds: Maronesa, a less-derived one; Fleckvieh, a derived one; and Heck cattle, a mosaic of derived and less-derived breeds. It shows that the Maronesa and the Heck bull are less derived in aspects like colour and horns, but that the morphological changes (reduced body, limb and head size, elongated trunk, reduced muscling, enlarged intestinum, reduced brain volume, changes in horn curvature and volume, enlarged appendages) as well as behavioural (trainability, reduced stress response, docility and lethargy compared to the wildtype) and probably the developmental changes causing them (changes in corticosteroid and thyroid metabolism, developmental delay and other factors) are universal to all three cattle exanimated, and possible all taurine cattle on this world as this is a look at both derived and less-derived cattle. There is the physiologic and genomic level as well, which cannot be tested based on photos. 


The looks vs behaviour problem and the Spanish fighting bull 

When looking at the breed Lidia, the Spanish fighting bull, however, it shows that Lidia is the least-derived breed in this respect. Lidia do have reduced body size, limb size and brain volume, but they are the one cattle breed in the world with the most wild cattle-like body shape. Especially young individuals have a muscular body with a slender waist, and they are the cattle breed with the largest hump. In essence, they look like more like hypothyreoditic aurochs rather than normal domestic cattle, which might indicate that the effects on hormone activity are not as intensive in Lidia as in other domestic cattle. However, whereas most domestic cattle have a drastically reduced fight/flight reaction, that of Lidia is very intense. The argument that the behaviour of Lidia is “unnatural” is baseless as we have no living aurochs to compare with and the very tame and docile nature of most other cattle breeds is not the wildtype state either. It might be that the aggression level of Lidia is intensified compared to aurochs but their aware behaviour is certainly more wildtype-like than lethargic docility. 

Considering that behaviour and morphology are interconnected via pleiotropy and developmental cascades, it would be an interesting question if it is no coincidence that the least-tame breed in the world is also the one with the most aurochs-like morphology. The farm fox experiment shows that most of the symptoms of the domestication syndrome go hand in hand with a selection on tame behaviour. This provokes the question whether a long-legged, athletic, long-snouted bull or cow that is shaped and coloured like an aurochs but still is more or less tameable and relaxed and not explosive in behaviour is a contradiction in itself. Maybe it is indeed impossible to remove all morphological vestiges of domestication (especially regarding body morphology and skull shape) by selective breeding on optical traits alone. In foxes, for example, conscious breeding for earlier maturity and larger litter size was unsuccessful, while selection on tameness resulted in exactly that. 

An interesting question that rises is whether Lidia always have looked and behaved like that since the domestication of cattle or if their ancestors were ordinary primitive cattle like other Iberian breeds that acquired this wild cattle-like morphology in the course of selection for aggression. 
Even more interesting would be the reverse test of the farm fox experiment with cattle: taking already aurochs-like cattle and selecting them on wildtype behaviour (more intense fight/flight reaction, shyness, explosiveness and other aspects) in order to see if they indeed re-evolve a wild type-like morphology. Such a project would require a different way of keeping them compared to grazing projects, but it would definitely be worth a try. 


A test for breeding-back: the Tamaskan dog

Since we cannot directly compare “breeding-back” cattle with the aurochs as it is extinct, it would be an interesting test for “breeding-back” to do the same with a domestic species whose wildtype is still extant in order to see if it is an efficient way to achieve the goal at all. This has basically been done with wolves and dogs in the form of the Tamaskan breed. The breed was bred using sled dogs, malamutes, huskies and German shepherd dogs in order to create a wolf-like appearance without any crossing-in of wolf dogs or wolves. The overall appearance of a Tamaskan is very similar to a Holarctic grey wolf, the matches in body size, proportions and body shape as well as colour are very wide-ranging. However, a closer look shows that it is clearly a dog. Especially head is larger and paedomorphic (snout, teeth size, eye size). The Tamaskan also has all other symptoms of the domestication syndrome: loss of acuteness of senses, earlier maturity and loss of seasonal reproduction, tame and trainable behaviour with greatly reduced fight/flight reaction. Wolfdogs, on the other hand, which are hybrid breeds of German shepherds and wolves, have a recognizable different behaviour. Tamaskan dogs display a usual domestic dog behaviour. Czechoslovakian and Saarloos wolfdogs are more independent than usual dogs, shy to strangers, easier to scare, need early socialization, have a strong hunting instinct, are more enduring and remarkably good at tracing. So there are morphologic, physiologic and behavioural domestic traits that breeding exclusively domestic individuals for a wildtype-like appearance could not eradicate. This leads to the question what “breeding-back” can achieve at all. 


What breeding-back can achieve 

Since wild and domestic animals differ dramatically on many levels (morphology, genetics, physiology, behaviour, development, endocrinology), and some basic key alleles of the aurochs probably went lost during domestication and thus “genetic breeding-back” is probably not feasible and the scientific framework is not done for it yet, and since classic breeding with domestic animals alone cannot produce a true reconstruction of the wildtype that lacks universal domestic traits, what can “breeding-back” achieve anyway? 
Looking at one of the best breeding-back results that have been achieved so far, the Taurus bull Lamarck, reveals the borders of breeding-back: It matches the aurochs in size and colour, the horns are good, the skull is OK, the proportions and body shape are good. However, it still has all the symptoms of the domestication syndromes: The muscling is still reduced and the intestines are enlarged, the skull is paedomorphic compared to a wild aurochs, the hump is reduced, as is the sexual dimorphism and seasonality of the reproduction circle in the population. Also its behaviour is comparably tame and relaxed. Therefore Lamarck is, albeit being rather aurochs-like in appearance, domestic cattle. The horn shape, body shape and skull shape could be improved by breeding, but the animals would remain domestic. 

The symptoms of the domestication syndrome have a millennia long history in the genetic architecture of the animals and cannot simply be reversed by selective breeding with these domestic animals alone. All in all, the maximum that can be achieved is a “bovine Tamaskan”. This might sound disillusioning, but a bovine Tamaskan would be more aurochs-like than it sounds at first and absolutely sufficient for the basic goal that is filling the niche of the aurochs with something very alike. Aurochs and cattle probably fulfilled the same ecologic niche (aurochs were probably better at digesting food and seizing the nutrients, but the food choice probably stayed the same). The social behaviour of aurochs and cattle probably is the same, as what we know of the aurochs is congruent with that of cattle and cattle have the same behaviour as living wild bovines, so the aurochs must have been the same in this respect. Cattle did loose a lot of fitness during their domestic evolution, but there are numerous examples of self-sustaining feral cattle populations that descended from rather derived breeds, so establishing wild populations of these bovine Tamaskans should be no problem as well. 

Thus, breeding-back results will always remain domestic, but they would be very much like the aurochs in many respect and would fill the niche of the aurochs successfully and authentically. And after many generations of dedomestication in the wild, they would become a new, post-domestic wildtype that resembles the pre-domestic wildtype to a large extent. 
And if we can genetically reconstruct an aurochs by cloning or CRISPR-Cas9, even better. What to do with a genetically reconstructed aurochs is covered here



Thursday, 24 October 2019

White spots in breeding-back cattle

Along with the Hornless allele, the alleles for white spots are among the gene variants definitely not wanted in “breeding-back” as white spots are a trademark sign for domestic animals of any species. However, the genes are in the pool for breeding-back. With this post, I want to have a look at how common they are and where they come from. 

The genetic background for white spots is complicated in cattle. It is important to note that the so-called colour-sided variant present for example in Texas Longhorn is caused by another locus named Colour sided and is different from the piebald pattern we see f.e. Fleckvieh or Frisian and breeding back cattle. The white streak on the face or forehead is caused by the KIT locus. A Spotted allele was coined which is claimed to be responsible for the piebald pattern, but the inheritance for white spots does not suggest a mere Mendelian trait. First of all, white spots seem to cumulate – many individuals might have just a few tiny white spots on the ventral side of their body, but when bred to another individual with white spots they get larger and more widespread, until the individuals are completely piebald. Furthermore, the inheritance of the spots is complicated and might also be influenced by sex (see the next section). 

Heck cattle (and Taurus cattle)

The number of Heck cattle individuals showing white spots on the belly or a streak along the face/forehead is not inconsiderable. You find a number of individuals with these traits on google. In Oostvaardersplassen, where no phenotypic selection occurs, such individuals are particularly widespread. There was at least one completely piebald individual reported (van Vuure 2005). I saw a piebald individual myself in the Lainzer Tiergarten herd in Vienna. Heck cattle has many colour alleles from its ancestral breeds, and white spots are among them. They were probably inherited from the one Black-pied bull Heinz Heck used (perhaps also Corsican cattle which carry the genes on occasion). 

Taurus cattle also may have white spots seldomly, for example the otherwise very good cows 42 508 and Lisette. Margret Bunzel-Drüke reports that the inheritance of white spots in the Lippeaue is curious – female offspring of cows with spots often have them too, while males tend not to. So the particular genes they have might be sex-dependent. White spots are comparably rare in the Lippeaue population, only a handful of individuals have or had them. In the Lippeaue, these might be inherited from all four ancestral breeds: Heck cattle, Lidia and Sayaguesa all may have the genes, and even Chianina where it would be masked due to the dilution alleles that make their coat completely white. 
Taurus cattle in Hortobagy, Hungary, also might have spots on occasion. This is because red-pied and black-pied bulls were used right before they were able to acquire Heck and Taurus bulls, and there is still a good-looking half-Holstein cow in the herd. The otherwise rather good-looking breeding bull Zseuz was selected out because it has white spots on the belly that transferred to its offspring. 

Tauros cattle 

Of the founding breeds of Tauros cattle, at least Sayaguesa have the genes for white spots, and at least one cow that I know of has one on its belly. A number of the Sayaguesa x Tudanca individuals has spots on the belly (go here). 

Auerrind

I have not seen any individuals with white spots in the Auerrind project so far, and it might be that there are none. However, the herd the Sayaguesa are from is the same as those of the Taurus and Tauros cattle project (Peter van Geneijgen), so it might be possible that the genes are in the Auerrind mix, but only future can tell. 

What does this mean for breeding-back? Actually only that white spots are simply widespread among domestic cattle in general. They are present in all groups and types of cattle and so also in breeding-back cattle. It is, however, the question whether individuals with spots should always be selected out or not. Surely no project wants that their cattle would end up piebald in the wilderness, such as the Heck cattle in Oostvaardersplassen. This is a complicated question as the genetic background of those spots seems tricky and unresolved and it is probably up to the individual breeder. However, if someone does not want white spots in any individual, they of course can select out each individual showing them. 

Monday, 21 October 2019

Controlled hybridization for saving the wisent?

Long-term readers of this blog will know that the second large wild bovine of Europe, the wisent, is an animal that is not only very spectacular to look at but is also immediately threatened by its extremely low genetic diversity. I covered this topic in several posts already (Overpurity as a danger for the wisentDonate for the Wisents in the Caucasus and What to do with the wisents in the Caucasus). 
I also repeatedly emphasized why I see the hybrid wisents in the Caucasus as a chance instead of a threat, and I also already introduced the idea of controlled hybridization with American bison in order to increase the genetic of the wisent. This is of course a provocative idea that sounds risky, but I have my reasons and I consider a careful way how to put it into practise worth a try. This is what I want to explain thoroughly with this post. 

The problem 

Inbreeding basically leads to a reduction of genetic diversity, which in turn leads to an increase of homozygosity in the genome. As long as the genome is purged off deleterious (harmful) alleles in the process a high level of homozygosity does not necessarily affect the healthiness of the population (such as in Chillingham cattle), but when the fixation of the alleles is coincidental, such as in the case of a population crash, the consequence is that a lot of deleterious alleles suddenly have a high chance of becoming fixated homozygously in the population, causing them to express their effects in the phenotype and thus leading to a so-called inbreeding depression. The consequences are increased frequency of diseases or distortions that can pose a long-term threat for the survival of the population. This phenomenon is well-known, not only to geneticists, and is a problem in the conservation of animal breeds and species.
The wisent is such a case. Due to habitat destruction and hunting, the population crashed at the beginning of the 20th century, and all living individuals descend from only 12 individuals. Nowadays, the inbreeding coefficient in the population is very high in both lines (the Lowland line and the Lowland-Caucasian line; the latter one partly descends from the last bull of the B. b. caucasicus subspecies). The inbreeding depression affects skeletal growth leading to skull asymmetry, deformation of the male gonads, increased rate of stillbirths, decreased female fertility and a reduced resistance against diseases and parasites. Wisents are particularly vulnerable to posthitis and balanoposthitis, foot-and-mouth disease, cattle tuberculosis, bluetongue disease and others [1]. Epidemics are an acute danger to wisent populations, both in the wild (in Bialowieza, 20% of the mortalities are caused by diseases) and captivity (few years ago, the stocks at German zoos crashed because of foot-and-mouth disease). Often, reintroduction efforts fails or experience painful set-backs because the animals are too sensitive to diseases (see the herd in the Romanian Carpathians). This is why the action plan for the conservation of the wisent still sees it in the danger of extinction [1]. The genetic basis is simply too narrow to ensure a long-term survival for the species. 

Possible solutions 

The current conservation strategy for the wisent is to continue line breeding without loosing diversity any further. This will not overcome the inbreeding depression but is an attempt not to make it worse. The only way to overcome the inbreeding depression is to increase genetic diversity by introducing more alleles to the population. Except from “constructing” artificial genetic diversity by altering the nucleotide sequence of extant wisents with genetic engineering (which I do not know of genetically feasible), I see only two possible ways to achieve that: acquiring genetic material from wisents that lived prior to the population crash (pre-bottleneck) and reintroducing it into the modern gene pool, or controlled hybridization with the closest living relative, the American bison. 

            Pre-bottleneck wisents 

The genetic material of any wisent that lived prior to the bottleneck event would probably increase the genetic diversity within the modern population greatly, even if it is only one individual, be it from the 19th century or anywhere else during the Holocene. It should not be impossible to acquire the full genome of such pre-bottleneck individuals. There are probably plenty of hides, trophies or skeletons gained from wisents during the most recent centuries that should all still contain enough genetic material. Also any skeletal remains from the latest millennia might be well-preserved enough for this purpose. Since it was possible to resolve the full genome from 8000 year old aurochs bones, the same might be possible with wisent remains. Once the full genome of one or more pre-bottleneck wisents is resolved, it would be possible to introduce the differing alleles into the genome of a recent wisent using CRISPR-Cas9 (the same method has been suggested to revive the woolly mammoth based on an elephants’ DNA). One or few individuals from prior to the end of the 19th century would probably (re)introduce enough “new” (or actually old) alleles into the populations to greatly reduce the effects of the inbreeding depression. The downside of this idea is: a lot of research work has to be done that is expensive and the technique is effortful as well. At the moment all the resources of these “de-extinction” techniques are concentrated on more prestigious animals such as the woolly mammoth, and it is pretty unlikely that anyone would spend a lot of money and effort on reconstructing old individuals of a species that still exists, even tough it would be a crucial step to saving the species. 

            Controlled hybridization with bison  

The second method, crossbreeding with its closest living relative, the American bison, would definitely be less costly and could be started immediately. It has to be said that both species are very closely related, they hybridize readily without any barriers or limitations and there are many authors that list them as one species. I am not suggesting to just rampantly cross all wisents on this world with bison and to swamp the whole population with bison genes. Not at all, this would be a huge mistake that would lead to the extermination of genuine wisents on a genetic level. What I am suggesting is wise and moderate hybridization followed by selective absorptive breeding on a separate, new breeding line with a separate herd book. The ancestry of each of these individuals would be documented just as that of the pure individuals. By this way, the population of the pure but inbred wisents on this world would not be affected or threatened in their genetic integrity in the least, only a few starting individuals would have to be “sacrificed” (if you would start with say, only 100 individuals, I bet this number would be still less than all the losses in the global population caused by inbreeding effects each year). 

The ultimate goal of the hybridization and subsequent breeding would be a population where the frequency of the deleterious alleles has been considerably reduced without affecting the biological integrity of the species too much by bison alleles. The deleterious wisent alleles affect development and other health factors and are probably not crucial for defining wisent characters. Thus, replacing them with alleles from bison would have a beneficial effect on the development and health of the individuals without affecting their nature as Bison bonasus. Of course hybridization will introduce any alleles of the American bison, which is why some sort of controlled breeding is necessary.  In the end, the animals would have to be indistinguishable from other wisents in morphology and looks, behaviour and ecology but at the same time not suffer from the same effects of the inbreeding depression as their conspecifics do. 

The American bison is subdivided into two subspecies, the plains bison Bison bison bison, and the wood bison Bison bison athabascae. Both subspecies are different ecotypes and have different phenotypes. The wood bison is more adapted to woody habitat, is better adapted to cold and is phenotypically not a far removed from the Wisent as the plains bison. So it would probably be wiser to take wood bison for the hybrid project. 

See here for a comparison between wood bison (left) and plains bison (right). As you see, the wood bison also morphologically resembles the wisent better than the plains bison. 

How to execute such a project 

The larger the initial gene pool the better of course. It would be easiest to start with a herd of bison cows and put a wisent bull on it, but the purpose of the project would be to gather as much wisent diversity as possible, so it would be wiser to start with a herd of wisent cows (20 would be minimum I would say, 100 would be ideal) and put a bison bull on it for the first round. After that and when all cows produced 50% bison and 50% wisent individuals, the American bull would have to be replaced with a wisent bull. The half-wisent individuals would be backcrossed with a pure wisent, which is called absorptive breeding. In order to gain maximum diversity it would be best to replace the wisent bull in each round, although this would be incredibly effortful and costly. This would have to be continued until 1/8 or 1/16 bison individuals are born. Depending on how strongly the bison influence shows, one of these advanced hybrid individuals could be chosen for breeding. I would only take bulls where the hybrid influence is phenotypically as much as undetectable. This is now where the real deal is going to happen: breeding between individuals that both have hybrid ancestry. Only the mating of two wisent that both have hybrid ancestry can enable the true purge of deleterious alleles from the population and the fixation of healthy alleles. The hybrid wisent bull would mate with the pure wisent, half-wisent, quarter wisent et cetera that are present in the herd. Personally I would phase out the individuals with a high bison percentage in this stage. When there is a good mix in the population with all individuals having a high wisent percentage in their genome, phenotypic selection can begin. It would be necessary to remove well-mixed individuals that have a clearly visible hybrid mark in their morphology and external appearance, or show bison behaviour such as head-butting in combat fights (wisent fight horn to horn like cattle). Factors such as food choice could also be evaluated, as bison are more heavy grass eaters than wisent, while wisent also like to browse and peel trees. Another round of pure wisent backcrossing might be necessary in order to get the wisent percentage in the individuals as high as 95% and higher. 
 
A schematic illustration of absorptive breeding
After couple of generations, the wisent would hopefully be virtually indistinguishable or even completely indistinguishable from pure conspecifics (there would be some individuals with bison traits popping out on occasion as usual in breeding, selection would have to wheedle that out in the long term run). What would be crucial now is actually the main purpose of the project after all: studying whether these wisent with bison introgression are truly more healthy and evolutionary fit than their inbred conspecifics. If my expectation is right, symptoms of the inbreeding depression such as stillbirths, infertility, developmental disorders and asymmetries must have decreased in frequency or maybe completely disappeared. Also, they would hopefully be less prone to the typical inbred wisent diseases. If kept under semi-natural or natural conditions, it would be very interesting to see if the survival rate in winter is higher than in Bialowieza, where most of the wisent die of the usual diseases that are plaguing the species. 
If the wisent with the controlled and selected bison introgression are truly healthier and more evolutionary fit than the pure but inbred ones, and indistinguishable from pure ones at the same time, the project could be called a success and the wisent would finally have a perspective for an ensured healthy long-term survival. 

A herd book 

Setting up a herd book would be essential in order to carry out the project in a professional and transparent manner. It would be separate from the international herd book for pure wisents, and it should mark not only the genealogy of the individuals themselves but also their genetic composition, f.e. 25% Bison 75% Wisent. Perhaps also if both parental sides have hybrid ancestry or if it is merely a back-cross. In this way, the introgression project would be absolutely transparent, controlled and documented, and there has to be no fear of a rampant, irreversible swamping of the wisent pool with bison genes. Especially since all evidently pure wisents are listed in the official breeding book for the species anyway. 

A breeding book for wisents with introgression from bison also opens possibilities for the Caucasus population, which descend from hybrids with plains bison. While there are voices that want to cull them all (f.e. such as the international wisent conservation action plan), the population could be regarded as being of considerable worth as it is the only large wisent population with a long history of living in the wild under natural selection on this world at the moment, and the bison hybridization increased their genetic diversity and probably also evolutive fitness.  A few herds of these individuals could be taken and bred in European conservation projects, but registered in a breeding book. That is where the hybrid project’s breeding book could be an option for the recognizing of this population as something of worth for conservation. A second section in the hybrid breeding book could be set up for this particular genetic line (the plains bison hybrids from the Caucasus), and the largest concern of the opponents of introgression in order to safe the wisent, the danger of confusion with pure wisents, would be refuted as everything is transparent thanks to the herd books. As the Caucasus wisent still show phenotypic vestiges of hybridization (if you take a close look, you see that they are somewhere intermediate between bison and wisent), they could be back-crossed with wisent again. In the long term run, it could even be considered to fuse both the wood bison hybrids and the plains bison hybrids in order to gain maximum genetic diversity. 

A hybrid herd book would also be a prospect for those wisent not registered in the official purebred herd book. There are about 700 individuals not registered because their pedigree is not proven or documented. A number of them might have hybrids with bison or cattle in their ancestry, a number might be pure but not documented. Anyway, conservation acts as if those 700 wisent would not exist, despite it is a considerable number and some of them might be more healthy than those in the official herd book. Ignoring them completely is maybe not wise. They could be included into the hybrid herd book as well, in the form of a third section. 

References 

[1] Mammal Research Institute, Polish Academy of Science: European Bison Bison bonasus: Current state of the species and an action plan for its conservation. 2002


Sunday, 20 October 2019

Second-generation Auerrind crosses underway!

After my portrait of the two subadult Auerrind bulls, Claus Kropp told me that Alvarez the Sayaguesa x Watussi bull has already inseminated the Sayaguesa x Grey cattle cow and soon will be brought to the herd of Chianina x Sayaguesa crosses. I am extremely happy to hear this as this not only means that next year we will see the birth of the first second generation Auerrind, but also that the very promising combination (Sayaguesa x Chianina ) x (Sayaguesa x Watussi) will be realized. 

The (Sayaguesa x Watussi) x (Sayaguesa x Grey) sounds promising too. It surely will have a lot of Sayaguesa characteristics, and also the potential for long and large horns on both parental sides. Thanks to Grey cattle, the winter coat has the potential to be rather good. 

I was also told that the first Chianina x Watussi have been born. This combination will also be used as a partner for Alvarez in the future once the newborn individuals are sexually mature. I am looking forward to see how this combination will turn out, and true F2 Chianina x Watussi would certainly be also worth a try (they would even have the potential for a perfectly aurochs-like colour: Watussi removes the dilutions, Chianina contributes the allele for E+ and black pigment, possibly even some degree of dichromatism masked under the dilutions). 

Now the project is really coming on, it is great to see it progressing with each year. A herd book exists since 2015, which is important for keeping track of the offspring. 

Wednesday, 16 October 2019

Two Auerrind bulls

Today I want to cover two of the most significant Auerrind bulls that are around so far: the Maremmana x Watussi bull Apollo and the Sayaguesa x Watussi bull Alvarez. Both are now old enough to deliver an idea what their body shape and horn shape is going to be like when fully grown, and their coat colour is final as well. 
 
© Auerrind Projekt
Apollo 
© Auerrind Projekt
The Maremmana x Watussi bull is exactly intermediate between its both parental breeds in looks. Alternatively, it looks like a red Maremmana bull with really thick horns. The body shape does show Watussi traits, but the zebuine hump is only very small. The horn shape is elegant with pointed tips and looks a lot like those of some Heck cattle of the Wörth lineage, which is not surprising as both share Watussi ancestry. It is larger than the grown pure Pajuna bull, but Pajuna is a small breed. 

Alvarez 
© Auerrind Projekt
© Auerrind Projekt
The Sayaguesa x Watussi bull is one of the combinations I was looking forward the most and it is very exciting to see this guy grow. The colour turned out perfect, it seems to have no zebuine hump or at least a very small one, the body shape is Watussi-influenced but not as sausage-like as in Apollo. The big question is how its horns will turn out – how large they will get and which curvature they will have. As the bull is still quite young but the horns have a large diameter at the base, I guess they might grow large to very large. 

Having had a look at these bulls it is of course fun and exciting to think about what kind of cows they could be bred into in order to produce good results. If Alvarez would be bred to a pure Sayaguesa cow, with look the result (75% Sayaguesa, 25% Watussi) would be very satisfying already. Bred into another one of its kind, the resulting true F2 has at least a chance to be stable for the desirable traits. One could also breed Alvarez to one of the Chianina x Sayaguesa cows, in order to have more genes for large size and long legs in the mix. Producing true F2 with this combination ((Sayaguesa x Watussi) x (Sayaguesa x Chianina)) might be promising. 
For Appollo, finding the right combination for promising offspring in the first generation is more tricky. One of the Sayaguesa x Chianina cows might be a worth a try concerning body size, horns and overall shape, although there is a high chance that the colour would be diluted (what would not be that much of a problem to me as colour is comparably easy to breed because it is controlled by only a few genes). 

The Auerrind project’s aim is to produce more stable results by using true F crossings (for the F-terminology, go here). I don’t know if this means that they would strictly cross only the breed A x B crosses with the same of their kind, or of they would also allow (A x B) x (C x D) and continue line breeding with true F of these combinations. I think this might be more efficient, as none of the cattle breeds selected would combine all aurochs traits in a two-way-combination. 

On the photo below you see Apollo, Alvarez and the fully grown Pajuna bull that joined the Auerrind project last year. I am happy that Pajuna has been included in the programme, although I do not know any efficient cross combinations with Pajuna in this selection. Maybe it can help to increase volume at a later stage of the project. 
© Auerrind Projekt