fuck

fuck

Friday, 29 January 2016

Dun factor identified - reveals surprises and confirms old suspicions

Finally I have the time and mood to write this post. Regarding the coat colour of Eurasian wild horses, historic reports give us a clue but are not always unambiguous. For example, there is room for interpretation what “tan” or “mouse-coloured” is supposed to mean, because the authors of former centuries certainly did not use the words in the sense of modern horse coat colour terminology. In previous posts, I summarized and analysed all historic texts on wild horse exterieurs available to me:

Due to the ambiguity of historic accounts, genetic research identifying coat colour genes from ancient DNA of predomestic horses provides substantial additional clues on the actual colour of European wild horses. The last one of the posts linked covers a crucial question. Previously it has been resolved that Pleistocene and Holocene European wild horses had both the Agouti A and a allele, which produce either a bay or black base colour. But these two loci do not determine the final colour that is expressed; the so-called dun factor works upon these two base colours, and produces the phenotypes bay dun (a colour that is certainly wild type since Przewalski’s horses and kulan-onagers show it as well), black dun (aka mouse dun, blue dun or grullo), plus the non dun versions of the Agouti colours. Sorrel is not relevant for us, because it is based on a mutation of the Extension locus that was seemingly not present in predomestic horses. The problem is that the dun factor was not identified until recently, so that the actual phenotype of these horses was not determinable. This table below shows all four possible colours based on the Agouti locus (never mind the leopard spotted, that’s another story) that I did for Wikipedia: 

Now, the dun factor has been identified in a paper by Imsland et al. a few weeks ago [2]. It was found that the Dun factor sits on a locus for the TBX3 transcription factor. Loss-of-function mutations on this locus cause developmental defects in humans and mice in the development of limbs, apocrine gland, tooth and genitals. This shows once again that “colour genes” are not only responsible for coat colour but a wide set of developmental factors (for more, see the Dedomestication series). The study used domestic horses, Przewalski’s horses, other equids and two ancient horses. One ancient horses is from Yakutia and 4,400 years old, while the other one is from Russia as well, but 42,700 years old. Now what is interesting is that the Dun locus houses three alleles: Dun (D), non-dun1 (d1) and non-dun2 (d2). Non-dun1 still shows vestiges of the wild-type markings, you can still see a dorsal stripe although the contrast to the surrounding hair is not that big. In non-dun2 horses, on the other hand, primitive markings are totally invisible. What is even more interesting is that non-dun1 was found to be a wild type allele too, besides Dun. The Holocene Russian wild horse examined was found to be homozygous for d1, so it might have been either bay or black in life (the Agouti locus was seemingly not tested, alas). The Pleistocene horse was found to be heterozygous D/d1. So that not only means that non-dun equines existed already back 43,000 years ago, but also that both these alleles were present in one population at the same time.
As an example for a d1//d1 horse, see this photo of an Exmoor pony that I took at the Exmoor Pony Centre. Exmoor ponies are, as far as I know, neither a nor A, but At/At, causing a condition called seal brown or dark brown. This allele has not been found in ancient populations yet. So if I interpret this correctly, considering the Exmoor pony’s colour a fully wild type colour would be speculative. For a d2//d2 horse, see this Noriker on Wikimedia commons.

Additionally to that, a considerable number of the predomestic horses tested in Pruvost et al. were found to be heterozygous A/a on the Agouti locus as well. This might implicate that in many predomestic Eurasian wild horse populations could have displayed all four possible colour morphs at the same time, the dominant ones possible more frequently than others (bay is dominant over black, dun is dominant over non-dun).

Although I suspected that, I find it surprising. I was actually hoping that the identification of the dun factor gives us a correlation between dun/non dun and a certain geologic age or habitat type, because it would make sense according to the camouflage effects the different colour morphs have (dun intuitively seems more suited to open habitats while non-dun fits forested, bushy landscapes in my subjective perception). However, if it is indeed true that there is no regional and geological correlation between the alleles A, a, and D and d1, wild horses of the ferus subspecies would be the only large herbivores displaying more than one colour morph in one population. It has been assumed that the homogeneity of wild animals, especially prey animals, is due to selection by predators because single individuals being coloured differently from the majority of the herd might be more attractive. Based on the current data, predomestic horses seem to violate this suspicion (I consider it merely a suspicion, I don’t know if it has been tested empirically).
However, there is another equine species that is known for occasionally showing deviant colour morphs, the Plains zebra (see this post).

I have been collecting a number of wild horse depictions in prehistoric art. I am going to present and analyse them here when I have the time to. Art, of course, leaves a much greater room for interpretation than genetic data. 

The authors also consider it likely that the zebra coat pattern is an extreme expression of dun plus wildtype markings [2].


[1] Pruvost et al.: Genotypes of predomestic horses match phenotypes painted in paleolithic works of cave art. 2011


Wednesday, 20 January 2016

New website and name for the Lorsch-Bielefeld project

Originally, the breeding sites at Kloster Lorsch and Bielefeld were part of the Uruz Project until a split last year. Now it is a project on its own run by the Freilichtlabor Lauresham and Förderkreis Große Pflanzenfresser Kreis Bergstraße (Kloster Lorsch) and Landschaftspflegebetrieb Hohmeyer (Bielefeld), and they still follow the plan of two-line breeding (Chianina x Watussi, Sayaguesa x Hungarian Grey/Maremmana). They are also thinking about experimenting with other combinations of these five breeds. A third herd is planned. 

The project has its own name now, Auerrindprojekt. Auerrind in German means basically the same as aurochs (Auer-ochse), just with "cattle" (-rind) instead of "ochs" as a suffix. Auerrind is not used as frequently as Auerochse, but it exists. 
The project also has a new website, in German: www.auerrind.wordpress.com. They are working on other language versions as well. 

This website includes a news section where they will regularly inform on the progress of the project, monitoring, introduction of individual animals and breeding sites, also with pictures. They started a herd book, so that the relationships of each animal to each other is documented right from the beginning.  

As I reported in the post linked above, the young Chianina bull "Bruno" covered at least one Watussi cow at Bielefeld last year, what means that we can expect the first Chianina x Watussi crosses to be born this year. 

Last week, two Maremmana cows arrived at Lorsch. The import of three Sayaguesa cows plus one young bull from the Netherlands is in progress. The Chianina herd at Lorsch is also going to receive a new young Watussi bull this year. 

So the Auerrindprojekt is really getting going, I am so much looking forward to see the first cross results. Sayaguesa x Maremmana/Grey might resemble some Tauros and Taurus crosses, while the appearance of a Chianina x Watussi combination is something that I am really curious on. 

Aurochs-coloured Chianina, once again

I did a post on the idea of how aurochs-coloured Chianina might look like a while ago. I did drawings by tracking out photos of a Chianina bull and a cow and coloured them in the wild type manner. But the drawings in the first post were rather sloppy. So I did new ones a few days ago:
Original photo of the bull and the cow
Colour is one of the most prominent traits of an animal that leap to the eyes when having the first glance at an animal. A completely striped donkey would look more like a zebra to us than a donkey, and vice versa. And an animal with aurochs-like colour but otherwise not many aurochs traits might look quite satisfying because that trait gets much attention. This is the case in for many Heck cattle that would otherwise look nothing like the aurochs. 
And the reverse is the case as well. A "wrong" colour might make the animal appear less aurochs-like than it is, because it distorts the image as a whole. So I tried to imagine what wild type-coloured Chianina would look like, and how it would accompany with the aurochs-like proportions and slender body shape the breed usually has. 
I think that wild type coloured Chianina would be quite aurochs-like. What would still be needed of course are horns of desired shape and size, they would also need larger heads with more elongated snouts (usually), as much as bigger humps. For cattle to be rewilded in colder parts of Europe, they would also need longer and denser winter coat. The winter coat of pure Chianina is sufficient for Central Europe (the Chianina in the Lippeaue do just as well as the other cattle in the reserve), but I think that a winter coat like Hungarian Grey, Heck cattle and others have is what can be considered the ideal case. 

Saturday, 9 January 2016

The full aurochs genome and inclusion of local aurochs into European cattle stock

With the full genome of a 6700 year old male aurochs being sequenced since 2013, it is possible to get better insight on the genetic relationships between wild aurochs populations and domestic cattle, if there was local introgression from wild individuals and which genome regions were particularly influenced by domestication. Now a summary of some recent papers.  

The whole-genome sequencing data placed this British aurochs as an outgroup to all modern European cattle [1,2]. mtDNA suggested that Southern European and North-Central European aurochs formed different genetic groups, the latter one being closer to domestic cattle than North-Central European aurochs are [3]. Perhaps hence the genetic distance of the British aurochs, but I tend to think that a southern European aurochs would be an outgroup to cattle as well.

Nevertheless, it seems confirmed that farmers did consciously breed wild aurochs into their stock. Orlando 2015 found that British cattle breeds (in particular: Highland, Dexter, Welsh Black, Kerry, White Park [2]) show substantial amount of admixture with British aurochs, sharing many polymorphisms [1]. This suggests that Neolithic farmers consciously bred aurochs into their stock, perhaps to gain local climatic and immunologic adaptions for their cattle (those which, after all, originated in the Near East) [1,2].
Orlando 2015 concluded: „Most European breeds apparently developed in situ with no mitochondrial influence from local aurochs, except perhaps Italy, Poland and Switzerland where B. primigenius mtDNA variants can be occasionally found in modern and/or ancient cattle. “

The case from Switzerland that he mentioned is described in a 2014 paper that reported the skeleton of a small female bovine standing only about 1,10 meters high at the withers, therefore being undoubtedly a domestic cow, dated to 5300-5000 years BP, but possessed a mtDNA P-haplotype variant of the European aurochs. Therefore this individual is the result of local admixture – and further not a first-generation hybrid because of its size. It again suggests intentional breeding with (female) aurochs [4].  According to Park et al. 2015, the Q haplogroup suggests limited local admixture as well [1]. It is important to note that no modern domestic cattle have the P mtDNA haplotype, which does not imply that all the nuclear genes introduced by the interbreeding were lost as well, as long the lineage did not vanish.

So now we have it confirmed that local aurochs did leave a genetic trace in European domestic cattle. Evidence indicates that it happened only rarely, but in my opinion this kind of evidence and the material we have is not able to determine the quantity of such events.
However, I see no reason to be euphoric over the results and draw conclusions like Italian or British cattle being more of an European aurochs than other cattle.  

An interesting side note: Park et al. 2015 detected traces of zebuine components in some Italian cattle (Chianina, Marchigiana and Romagnola) and East Asian cattle (Hanwoo and Wagyu). But it is also possible that those are alleles that other taurine cattle have lost [2].

It was found that domestication affected genes for neurobiology, growth, muscle development, metabolism and immunology [2].

Last but not least, an interesting passage from Orlando 2015 that brings up some aspects of domestication that might not be that often considered:
„Animal domestication is, however, likely to not just have remodeled the sequence of the
 genome. Micro- biomes, for example, might also have changed in relation with dietary
 shifts, which possibly affected important phenotypic traits, ranging from the physiological 
to the behavioral. As wild and domestic animals show subtle changes in brain gene 
expression networks, transcrip- tional changes are also likely to have been an early
 component of domestication.“

References

[1] Orlando, L.: First aurochs genome reveals the breeding history of British and European cattle, 2015.
[2] Park et al.: Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. 2015.
[3] Lari et al.: The complete Mitochondrial genome of an 11,450-year-old Auerochsen (Bos primigenius) from Central Italy. 2011.
[4] Schibler, Elsner & Schlumbaum.: Incorporation of aurochs into a cattle herd in Neolithic Europe: single event or breeding? 2014.



Monday, 4 January 2016

Post #200!

This is my 200th post. I have been blogging for two and a half years now, it has been a lot of fun doing research, “field trips” and artworks for this blog. I thought it was time to do a little retrospect on what I have published here so far to give you an overview, also for readers that have not been following my blog for so long but might be interested in some older articles.
I actually intended to read and correct form and language, but unfortunately I don’t have the time to do it thoroughly. Many of the pictures used in the posts became not displayed at some point due to either a change of html or errors by blogger. It’s annoying and I was not able nor had I the time to restore all of them. I apologize.  

My first entries in May and June 2013 were rather modest. This post
The various breeding-back efforts provides a quick overview over the most important breeding-back attempts. However, it should be a bit more comprehensive and I might do a new one one day.
This article What is breeding-back all about? introduces what breeding-back is about and what good there is in it. Note that I used the word phenotype synonymously with morphology and looks back then, which is imprecise. This term actually describes everything that is expressed by the genotype and influenced by environment, and therefore also includes factors such as behaviour.

Most post on my blog, perhaps up to 80%, are about the aurochs. Not because I am incredibly obsessed with this animal, but there is much more to write about. Concerning the European wild horse, I covered everything I have references for already unless new research delivers new data. Furthermore, there are no breeding-back projects for this species, and also are not necessary because we have breeds that already are what we want for the aurochs. For the quagga, I already gathered and posted all info I have about the quagga itself as much as the QP, but I keep on looking for new.
I have been planning to do more species diversification here for long, but I think everything we can say about the European wild ass and the European water buffalo is said in my posts already, until new evidence shows up.

Now I am going to present the most relevant posts per category.


General articles

A little article on what I find so fascinating about the whole subject, but also what it is all about and what good it serves after all.

Why doing breeding-back at all? A similar themed article.

“Effigy breed” is an attempt of mine to translate the German Abbildzüchtung as a neutral term for the result of “breeding-back” (or in this case “effigy breeding”) that does not acclaim to reconstruct the whole species/wild type. I am not so happy with that term, which is why I don’t use it that often anymore. The post is about if there is a relevant difference between the result of a breeding-back attempt and a primitive landrace.


Quagga

The quagga and the Quagga Project introduces the quagga and its evolutionary background and systematic position, as well as the Quagga Project. I go into the project’s methods and in how far the project’s zebras can resemble the quagga.

A little personal prognosis in form of a drawing.

A collection of photos of all 23 preserved quagga skins.

The Quagga Project stud book plus photos of some beautiful individuals.


New quagga reconstruction, based on the mare at London Zoo The mare at London Zoo was the only living quagga that was photographed, and I used GIMP to do a coloured copy as accurate as possible, and I am satisfied with the result.

In this entry, I review the argumentation of the quagga project and give my personal opinion, i.e. that the quagga cannot be revived this way and that their zebras should be called “Rau zebras” instead of “Rau quaggas”.

This post presents a very time-consuming illustration of the coat colour variation within the preserved skins of quagga individuals.


Wild horse

The name “Tarpan” is a controversial and ambiguous one, and this post explains why. Nowadays I try to avoid this problematic term.

What the Tarpan looked like is a question that is not easy to answer, and I did a few weeks of research for this post and illustration. It is based on contemporaneous written accounts and scientific literature including modern genetic research.

The Tarpan that wasn't - the famous “Cherson Tarpan” which was photographed, a stallion of uncertain identity.

I took the effort to type all passages C.H. Smith wrote in his The Natural History of horses, with Memoir of Gesner (1841), with a short conclusion.

Where European wild horses dun-coloured or not? Another question that I approached by researching contemporaneous literature and modern genetic research. Recent publications might provide a little update – post upcoming.

This post is on the Pleistocene wild horse skeleton from Denmark, and I compared its skull to that of other horses and found that its skeleton seems to be identical to that of a Przewalski’s horse, not so much that of a Sorraia. The pictures in that post are gone, unfortunately.  



An arbitrary collection of horse breeds that I considered tarpan-like back then.


The Konik is not a breeding-back result I give a bit background info on the origin of the Konik, which is in fact not the result of a breeding-back project in the usual sense.

Defending the Konik against an unfair critique Title says everything. I don’t say that I have the truth in this entry, but just present the references I have and what extrapolations I made.

An introduction to the Heck horse, which amalgamates more and more with the Konik in Germany at least.



A collection of British ponies that I considered primitive back then, with some genetic and historic info.

Exmoor vs. Konik - which one is better? My opinion on that debate.

The Sorraia - is it a wild/ancient horse? In this entry, I took the arguments that Sorraia advocates use to give it a wild horse status and confront it with data from genetic studies, bone material and the breeds’ history, and draw my own conclusion on the nature of the Sorraia horse.

I checked my statement that the skulls of Sorraia horses are slim instead of robustly built by having a look at the Denmark skull and comparing it with some Sorraia heads. I came to the conclusion that the difference is not that big.

Subsequently, I did the same with the skulls of these three horses. The Exmoor and Konik skulls in this very small sample turned out to be quite alike.

Back then, the history of the Exmoor pony, especially as it is portrayed in Susan Baker’s book, made me presume that there was a kind of “British primitive horse”, a type or population of feral, primitive ponies that were once widespread in Great Britain and formed the base of most British pony landraces. The Exmoor pony would be the least diluted one, but is rather inbreed, so I suggested to build up a second gene pool using land ponies bred to resemble it.

Is the Exmoor less special than we used to think? A very interesting, down to earth publication from a few years ago put that “British primitive horse” idea strongly into question, and the Exmoor pony is seemingly not that special as we used to think.


Domestication, dedomestication and feral animals

http://breedingback.blogspot.co.at/2013/06/the-surviving-capacity-of-horses-and.html
A general post, that covers a number of feral horse and cattle populations to show that not only primitive landraces but also surprisingly derived domestic animals can feralize easily.

The dedomestication series:
I did a lot research on pleiotropic effects, developtmental cascades and endocrinological processes that might be related to domestication and the morphological changes that it causes, mainly inspired by the Farm fox experiment. I also had a look at feral populations of several species, especially the OVP Heck cattle, which I used as a model. With all that, I developed a concept on dedomestication and what implications it might have for breeding back. This concept, however, is on empirically weak grounds, also because dedomestication is an under-studied, neglected subject.

Markus Bühler corrected me on some things I wrote about feral pigs in my DeDo-series.

Piebald deer are interesting because they seemingly show the same mutations that cause the same piebald patterns in domestic mammals.

Domestication can change diet in mammals presents a paper that found that dogs differ from wolves in a number of genes involved in starch digestion and fat metabolism. Whether this is really caused by artificial selection or if dogs might inherited that traits from wild ancestors that differed from wolves already is a question treated in a separate post on dog domestication.

Aurochs horns at Oostvaardersplassen shows photos of Heck cattle at OVP that display an aurochs-like horn shape with an inwards-curve more strongly and elegantly expressed than in any Heck cattle outside the reserve. If it is a real trend, it is probably due to selective pressure for mechanically useful horns in intraspecific combats. Interestingly, only cows have truly inwards-curving horns yet it seems.


Cloning



The extremely low genetic diversity in the gene pool of the wisent is a life-threatening danger for the whole species. In this entry I suggest that cloning ancient wisent from ancient DNA would greatly increase the genetic diversity and therefore greatly improve the health of the species.




Other species

A slightly grumpy review of the DVD-version of “De nieuwe wildernis”, a documentary film of Oostvaardersplassen.

The Tamaskan dog as a test for "breeding-back"Actually, the Tamaskan dog is rather similar to breeding-back attempts.

Hybridization is damned in species conservation, while over-purebreeding is enhancing inbreeding depression. In this article, I defend the Wisent population in the Caucasus and suggest to set up a third breeding like for wisents with controlled, planned American bison introgression. Also I propose that additional research should be done.

I consider the Wisent population in the Caucasus an important one, and you can donate for them on the link I provide in this post.

Is the wolf a domesticated dog or something different? I did some research on dog domestication, and the origin of the domestic dog might differ a little from the traditional scenario. It was one of those article that were fun to do because I had to dig through a lot of literature and it became rather long.

This post includes everything that I can say about Bubalus murrensis.

And this post includes everything that I can say about Equus hydruntinus.

Some colour morphs within the modern Plains zebra population.


Aurochs

I can't give a comprehensive description for all those articles because it would occupy too much space, therefore I mostly just put the links. 

Just for starters.

A little post on the aurochs’ head morphology.

Forelocks and manes were another characteristic trait of the aurochs’ head.



I did reconstructions of 22 aurochs horn pairs based on fossil/subfossil skulls.

Female aurochs remastered My reconstruction of the Sassenberg cow that I consider most accurate. 



In 2015 I asked paleoartist Joschua Knüppe to do an aurochs reconstruction because there is so few correct aurochs art: Aurochs bull by Joschua Knüppe

This is my most recent reconstruction of that enigmatic subspecies. I list what we know of the Indian aurochs and what I deduce for its life appearance.

My first reconstruction of B.p. indicus, and if a “breeding-back” project with zebu could be done.

A photo of a primitive-looking zebu cow from Sri Lanka provided by Jochen Ackermann; today I think it could be the result of taurine influence just as well.


I tried to develop a simple way to objectively score cattle breeds for their resemblance to the aurochs, which is rather tricky.

An article that became surprisingly popular (4500 clicks), with a conclusion that I still agree with.

A table of Heck cattle’s founding breeds, under the assumption that none of Lutz Hecks’ Berlin stock were included.


In 2013 I met with Walter Frisch, the creator of the Wörth/Steinberg line (Heck cattle special for sometimes superb horns and comparably stable) and took a look at his herd. It was very nice, and the post includes a lot of photos.


A short list of aurochs-like cattle that is surely not complete.



History lesson pt.I: Please stop claiming Heck cattle was bred using the Spanish fighting bull ... under the assumption that none of Lutz Hecks' Berlin stock contributed to the population post 1945. 



  
Taurus cattle in Hungary are an interesting but unfortunately less accessible population to me. 


Visiting Taurus cattle at Lippeaue, Germany. My firt trip to the Lippeaue. 

The skulls of two Taurus bulls I own the skulls of two Taurus bulls, and for this post I did a lot of anatomical comparing with aurochs skulls. Also with informative photos. 







We keep comparing living cattle with skeletons of the aurochs. Actually, that's comparing apples with bananas, therefore I tried to deduce what the skeletons of certain breeds would look like. 

Aurochs-like Italian cattle are somewhat overlooked. 




Inbreeding as an option to fixate aurochs traits? I elaborated an inbreeding-based breeding method to create a genetically homogeneous, as aurochs like as possible line to improve other herds. 

Hairless bison, yak and fluffy aurochs Just some anatomical sketches to better compare the morphology of those four species.