Wednesday, 28 November 2018

Wild horse colour table by Maija Karala

The Eurasian wild horse subspecies, Equus ferus ferus, was, according to genetic research, not uniform in colour as most large mammals but displayed a number of colour variants. These have been summed up in this post. Paleoartist Maija Karala published a wonderful table on deviantArt showing all colour variants suggested by genetic data and ancient cave art (please do not use without permission): 
© Maija Karala
On dA, you also find a comprehensive description:
I especially like how the leopard spotted pattern has been illustrated, that way it looks really credible for a wildtype animal. 
I only have two remarks. As far as I know, the black phenotype suppresses the expression of pangare/countershading, so the black horse should be wholly black, and the chestnut allele e is, as far as the literature that I know, is a mutation in domestic horses that did not show up before the Holocene. 


Ludwig et al. 2009: Coat color variation at the beginning of horse domestication
Sandovall-Castellanos et al. 2017: Coat colour adaption of post-glacial horses to increasing forest vegetation. 2017. 

Saturday, 24 November 2018

Wrong use of genetic nomenclature in "breeding-back"

I have noticed that a lot of genetic terms have been kind of misused in “breeding-back”, and I was guilty of that myself in the past. It should always be paid attention that technical terms are used in the true conventional meaning of the word. In this post I give a little overview over the terms that I have noticed to have been used wrongly (and I used wrongly myself in the past). 

Phenotype: While “genotype” is quite clear, there might be a misunderstanding of what a phenotype actually is. A phenotype is not just the looks or the physical morphology of the animal, but every factual aspect of the living organism – its morphology, its physiology, its behaviour et cetera. So when you talk about a bull with a “good/suitable phenotype” you are also talking about its behaviour and all other aspects. The phenotype is not only influenced by the genotype alone but also environmental and epigenetic factors, and the interesting thing is that there is mutual influence between those factors. 

Ecotype: Not everything is an ecotype. An ecotype refers to a variant, population or subspecies of a species that differs from the others primarily in ecological respects. Most ecotype examples are found in plants, and not so many in animals (Wikipedia, for example, lists only a few whale species). One could say domestic animals are “ecotypes” of their wildtypes, but they also differ fundamentally in morphology, behaviour and genetics and not only ecology, that is why they are classified as different subspecies/populations/species and not ecotypes. 

Gene/allele: Not everything is caused by a particular “gene” or “allele”. Many times traits are multifactorial and caused by a number of genes, and very often a trait is just influenced by pleiotropic effects, development and phenotypic plasticity. For example, I can say with 100% certainty that there is no “allele for long snouts” or “allele for robustness” et cetera. Using a very technical language but at the same time exposing a rather simplistic conception of how an organism comes to shape is slightly absurd. 

P, F1, F2, F3….: The filial generation terminology is actually only used for a strict scheme of crossing: two animals of a different genotype, the P(arental)generation, are crossed with each other, the result is called F(ilial)1individual. Two F1 individuals produce an F2 individual and so on. When an F1 individual is crossed with an individual of the P genotype, it is called a B(ack-cross)1individual. The F-terminology is used commonly in “breeding-back”, but not always correctly. For example, Lamarck – a cross between a pure Sayaguesa cow and a Heck x Chianina bull – is a second-generation crossbreed, but not an F2 because its parents are of a different genotype. It is not a back-cross either because Sayaguesa is a third genotype beside Chianina and Heck of the parental generation. Actually, if you want to apply the F-terminology forcefully here, it is an F1, a cross of genotype A (Sayaugesa) and genotype B (Heck x Chianina). Its son Londo, a third-generation bull, was a true F2 as its parents were of the same genotype. This is where it gets confusing, which is why I do not use the F-terminology for “breeding-back” results anymore. 

Back-crossing: this concept is explained above and should not be confused with “back-breeding” or “breeding-back”. 

Monday, 19 November 2018

Cattle are "designer aurochs"

I have been doing posts on the organismic differences between aurochs and cattle lately (go here for an in-depth coverage of these differences, and here for a test of “genetic breeding-back”). Here comes another one, this time applying what I have outlined in the previous articles on particular cattle breeds and individuals.

Actually, I have been using a wrong dichotomy in all of my previous posts: cattle and aurochs. There is no distinctive line between these two animal types. Aurochs were snatched out from the wild and slowly transformed into domestic cattle in a fluid process with all kinds of intermediate stages. And in the end, even the most-derived modern domestic cattle would probably still be able to reproduce readily and successfully with aurochs and they still do share many characters in morphology, ecology and behaviour. This is why they are still considered members of the same species by most authors. More precisely and correctly, cattle are man-made modified designer aurochs– nothing more and nothing less. “Cattle” is just the term which we use to refer them to. 
So let us forget the word “cattle” for this post and analyse three examples of those extant modified designer aurochs: one example for comparably un-derived (“primitive”) breed (Maronesa), a rather derived breed (Fleckvieh) and a classic breeding-back result, a Heck bull. Let us not care about the history or “tag” of the breeds themselves (“landrace”, “derived breed”, “breeding-back result”) or the purpose for which those animals have been bred, but only the organismic and evolutionary state of these animals. 
I think this is important to get a better understanding of what those animals actually are from a fact-based, organismic-evolutionary perspective.

Before we take a look at the modified designer aurochs it is important to remember what the wild aurochs looked and were like: 

It was a swift and agile animal that was probably only to a certain extent tameable and trainable and also had a considerable aggression potential. It was seasonally adapted and fit to permanently being exposed to weather, disease and injuries. As a wild animal, its genome was comparably diverse. The dimorphism between the sexes was well-marked and the population was more or less uniform in its basic morphology. 

Maronesa bull 
© Goncalo Figueira
This individual is of a less-derived population. At first glance, this modified designer aurochs bears quite some resemblance to wild aurochs. The colour is exactly identical, indicating that it has the same alleles on the respective colour loci which also have functions in metabolism and neurology. The horn curvature is very reminiscent of the wildtype, any differences might be linked to developmental delay except for the fact that they are oriented lower relative to the snout. The morphology of this modified designer aurochs bull, however, reveals some deep-going changes in this individual. The limbs and the skull of the bull are considerably shortened or reduced in size, the brain volume is reduced as well most likely as a consequence of an affected thyroid hormone production or activity. Furthermore, the belly and intestinum is enlarged and the muscling reduced, probably as a result of an altered corticosteroid level that might be linked to its drastically reduced fight/flight reaction. The size is decreased considerably (about 140cm instead of 170 cm), probably due to developmental changes and conscious selection for smaller size. This modified aurochs is, in contrast to its wild conspecifics, tame, agreeable and it is possible to tether or use it for draft work – what you could never do with a wild aurochs. Probably as a result of developmental delay, the skull shows paedomorphism: the snout and frontal area is shortened considerably, the head has a concave profile and the eyes are enlarged. The sexual dimorphism is slightly reduced as well: while bulls, like this one, are always black in colour and considerably larger than the cows, some cows have a very dark brown colour or bull colour. It also has enlarged skin flaps and scrotum. Despite having a number of superficial similarities, this bull is an animal rather different from its wild ancestors from which it diverged about 8.500 years ago.

Fleckvieh bull
This bull is from a very derived population. Despite being larger than the Maronesa bull (between 150-158cm) and having a not as paedomorphic skull, its morphological modifications are more intense: the legs are even shorter and the skull smaller, the belly and intestines are enlarged considerably. The hump formed by enlarged processus spinosi almost completely disappeared. The horns dramatically shrank down in size and lost their curvature, probably as a result of both a developmental delay and mutated alleles that reduce the horn size. The sexual dimorphism in size and colour is strongly reduced. The colour of this modified designer aurochs is almost nothing like that of the wildtype as well. As a result of mutations on the KIT locus, which is also involved in neurology, it has unpigmented areas widespread among its body (piebaldism). Also, it has a mutated allele on the Extensionlocus that disables the production of black pigment, eumelanin, and causes a red fur colour and leaving skin areas such as eyelids and nose more sensitive to UV radiation. Like in the Maronesa bull, its behaviour is tame, trainable and lethargic compared to the aurochs, even more so than in the less-derived bull, which is probably a result of the altered hormonal levels and neurology. These modified designer aurochs are also less resistant to cold and diseases, their winter fur is shorter and less insulating than that of wild aurochs and less-derived cattle. Its natural instincts are also reduced; cows tend to calf in the middle of the herd instead of in a shelter, and they reproduce all year round. As a result of intense (in)breeding, the population of this bull carries a higher of deleterious alleles responsible for a number of diseases and disorders. This modified designer bull is, as a result of intense domestication, far removed from wild aurochs in morphology, physiology, behaviour, development, endocrinology and evolutionary fitness. 

Heck bull 
© Friedensgruppe Moos
This individual is from a population that is a mix of derived and less-derived breeds. It is just as small as Maronesa (about 140cm in height at the shoulders). As a result of altered development and endocrinology, limbs and skull are reduced in size, the trunk is elongated, the hump disappeared almost completely, the muscling is reduced and the belly and intestines increased in size. The skull is rather paedomorphic and it shows asymmetry, a possible consequence of inbreeding in this particular line. These morphologic changes go hand in hand with modifications of behaviour. As the other two examples, these are tame, lethargic, agreeable and trainable compared to the wildtype. The horn volume matches that of wild aurochs, caused either by new alleles, wildtype alleles or a mix of both (I consider the third variant the most likely) but the curvature is way weaker than in wild aurochs bulls resulting in more wide-ranging horns which is typical for domesticated bovids. The sexual dimorphism in this population is reduced, showing in bulls occasionally having a colour saddle like this one or bull-coloured cows. Rarely, individuals also might be heterozygous or homozygous for mutations on the Agoutiand other loci, resulting in a diluted coat colour. Some individuals also carry the allele(s) for white spotting on the forehead and belly – in homozygous state, the individuals might be completely piebald. Like in most domesticated aurochs, their seasonal adaptions are reduced; calves might be born during winter. Also, some individuals have their natural instincts more reduced than others, resulting in some cows calving in the middle of the herd while others seek for a shelter. This might be the result of the mosaic ancestry of this population. 
Despite having similarities to the wildtype in coat colour and horn shape, this bull is clearly a domestic animal in every respect. Additionally to that, it shows a mix of derived and primitive characters in both morphology and behaviour, which must be the result of its mixed ancestry. 

Genetic similarities. As you see, the similarities to the aurochs even of very aurochs-like breeds are comparably limited as the domestic nature of the animals simply prevails if you take a look at the organism as a whole. An important aspect would be if the differing extent of domestication between those three breeds would also show in the genetic distance to the aurochs. I believe it would, as phenotypic traits are (to largest extent) a product of the genotype. Now the question is how much and how they would differ in this respect. One possibility is that the more-derived breeds differ from the aurochs on more loci than the less-derived breeds, so that their genome carries more mutations than in the primitive breeds. In this case, the “genetic similarities” would be easily quantifiable. The more loci with original wildtype alleles, the more aurochs-like and less-derived. But there is another possibility. It might also be the case that the number of loci carrying mutations does not differ that much between the breeds, but the more-derived breeds have other mutations on the respective loci that cause a more dramatic effect than the mutations of the primitive breeds. And the third possibility is that the number of affected loci and the mutated alleles do not differ that much, but the more-derived breeds are more often homozygous for these mutations than the less-derived breeds as a result of more intense breeding. As usual, the reality is probably a complicated mix of all these three possibilities. 
Genetic tools that are used in standard procedures that are to measure genetic distance or phylogenetic relationships between evolutionary clades, such as phylogenetic markers (haplotypes on gonosomal or mitochondrial DNA) or SNPs are something that I do not care much about here because of their little relevance for the differences between a domestic animal and its wildtype (for more on that, see here or the posts linked in the first paragraph). They are easy and cheap, but say nothing about the defining genetic and organismic factors in question.