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Saturday, 28 March 2015

Please don't call it quagga


Don’t get me wrong, I am happy that there is something like the Quagga Project, and I like their current breeding results. But they make a number of claims that I simply cannot agree with. The Quagga Project pretends that they are able to – or even did already – recreate the quagga by selective breeding with extant Plains zebras.
They argue that since the quagga nowadays is classified as a subspecies of the Plains zebra it might even be only a colour variety with the only features making it distinct being the coat pattern. Furthermore, they say that since it was not a species on its own, the genes responsible for their colour scheme might still be present in extant Plains zebras just have to be united. And since the quagga displayed individual variation regarding the intensity of their stripe pattern, a rough overlap with the original and not necessarily a total match is required to call their results “quagga”.

However, the extinct quagga was not a zebra species of its own but one of several subspecies or local forms of the Plains Zebra. This fact makes a big difference - the quagga’s extinction may not be forever!
[The Quagga was]A variety of zebra […]
However, since the coat -pattern characteristics are the only criteria by which the Quagga is identified, re-bred animals that demonstrate these coat-pattern characteristics could justifiably be called quaggas.
[…] Therefore the Quagga and other Plains Zebras belong to the same species and consequently the Quagga should be considered merely a different population (or deme), of the Plains Zebra.
[…]There are a few Zebras which qualify - not as true quaggas, but as Rau Quaggas in the project. From our point of view they are "real" quaggas, but since there has always been the possibility that there might have been other features of the original quagga that we have not selected for (because we do not know what those features, if any, might have been), we have chosen the term "Rau quagga" to describe our recovered phenotype. Rau quagga is the name we chose to apply to animals which meet the criteria of no scorable stripes on the hind body and effectively none on the legs (Darwin recorded occasional stripes on the hocks in some quaggas, so we allow that in the hind legs). More will doubtless come along as time goes by...”

The project claims that the quagga was merely a colour variant of the plains zebra as they see no differences between the existing subspecies other than the colour. However, there never was an osteologic study comparing the morphological similarity between the plains zebra subspecies including the quagga. There were craniometric measurements with conflicting results (I assume that the authors of these studies took care of whether the skulls were from quaggas indeed or from horses and donkeys for taxidermies) – some studies suggested that the skulls of the quagga were nearly identical to that of other plains zebras, while others suggested they differed from those of horses, donkeys and zebras to the same extent. I learned from a skull gallery by Vera Eisenmann that there is quite some variation regarding skull shape within an equine species, so that factor might not be that important.
As to genetics, the quagga is nested within the plains zebra. That means, it is either a member of the species, or, if you consider it a separate species, descended from the plains zebra at least. It seems that the quagga diverged from the other subspecies in the middle Pleistocene [1], which is about the same time distance as between domestic horses and Przewalski’s horses. The quagga does not share any mitochondrial haplotypes with other plains zebras, but the sample size is probably too small to ascertain whether it indicates that it was a reproductively isolated clade on its own or did indeed represent the end of a cline as the coat patterns within the species suggest.
Nevertheless, I think that the divergence of about 200.000 years is too long to regard the quagga merely as a colour variant. Genetic drift inevitably leads to changes. Apart from that, you could argue in the same way that the hooded crow is “just a colour variant” – we have exactly the same situation here. Furthermore, the sparce molecular data does not give us any clue on the karyotype of the quagga – it might have one or more chromosomes more or less than other plains zebras, as it is the case in the Przewalski’s horse compared with the domestic horse.
We cannot say whether the quagga had any ecological differences to other plains zebras, but I don’t think it was necessarily the case. Not much is reported on their behaviour, apart from that they had an idiosyncratic call was an inspiration for the animal’s name (f.e. “kwahaa”), remotely resembling a donkey’s. 

My belief is that there is also a certain misunderstanding of the concept of a subspecies when they say: “the extinct quagga was not a zebra species of its own but one of several subspecies or local forms of the Plains Zebra. This fact makes a big difference”. A subspecies is, as the term implies, a less-marked form of a species, or as Darwin called it, an incoming species. Everyone who has basic biological knowledge will know that giving a clear, unambiguous definition of a species and therefore also a subspecies is highly problematic. But what can be said is that a subspecies is not just a result of taxonomical boredom or nit-picking, but an actual clade and defined by biologic criteria, and this is clearly the case in the quagga. As outlined above, there are more differences between the quagga and the remaining subspecies than pelage characteristics, such as genetic distinctions that inevitably must have arisen during about 200.000 years of separation, and its distinct call. Currently there is not evidence for more as far as I know (as if it was not enough). But the project argues that if there is no further evidence, no further defining characters should be assumed and therefore something that shows all traits that we know is automatically a quagga. In my opinion, the assumption that only those distinct features that we know of through our limited access were the only ones is ultimately destined to fail. However, the QP does not deny that the quagga was different (and it was certainly the most distinct of the plains zebra subspecies), but their assumption is that mimicking those traits that were unique to it and eradicating those that differed should lead to a true quagga.
Different genetics and different descent, different animals. No living herd of plains zebras do descend from the quagga in any way. The QP’s point is that all the traits that defined the quagga might still be present in the extant population thanks to the fact that they belonged to the same species and it likely represented one end of a cline. I see problems in this guideline: We have no clue on the factors that control the pelage characteristics in the plains zebra, which is the only trait the QP is focusing on. Is it polygenetic, or regulated by one gene only? Which characters is it connected with? No extant plains zebra has a stripe pattern that is as reduced as in most of the quaggas, not to speak of the brown background colour, so the selective breeding program is not working on a fixation of a trait but on trying to achieve it in the first place from what is not there yet. It’s like selecting for cattle with 100 cm horn length when starting with horn lengths of 50 and 70 cm. But if I interpret the QP’s argumentation correctly, they assume the amount of striping in a zebra’s coat is regulated by a number of genes, and that those alleles that worked in the quagga are split up among those we see among other subspecies, present somewhere towards the middle of the cline.  That’s a legit hypothesis, although a speculative one.

This provides a good opportunity to test the guideline of the QP. One could take some strongly striped zebras from Etosha and select them for a stronger stripe pattern. Would anybody claim that, if after some decades of breeding such a herd is as strongly striped as possible, a Grant’s zebra (E. q. boehmi) comes out? Or taking wolves, would picking a bunch of white or crème-coloured Northwestern wolves (C. l. occidentalis) result in a polar wolf? I think these examples show how simplified this concept is.  

However, let’s take the QP’s argumentation for granted for a moment and say that a Plains zebra that looks like the quagga automatically is a quagga, and that there are no external differences other than the pelage characteristics. Do the most advanced current results of the project look like quaggas in this respect?  
Judging from the remaining quagga skins and those individuals of the QP that I know, it is true that indeed a number of those zebras show a stripe pattern that is as reduced as in the quagga (apart from the legs, which are not yet totally stripeless). However, I noticed a not negligible difference regarding the stripes on head and neck. In the quagga, they are packed closely together, being broad while the white space between them is thin. And there are no thin stripes between broad stripes as we see it in many extant zebras. In the zebras of the QP, the exact opposite is usually the case. I even get the impression that as stronger reduced the striping on the rear is, the more it is on the face as well. The facial stripes in the quagga on the other hand were very broad and intense, giving the head a dark aspect overall.
The QP admits that there has been only little progress in achieving a brown background colour on the trunk. This might change in future generations, but maybe not. Maybe the last few stripes on the leg will disappear, but maybe not. Perhaps the climax is reached already, only future will tell. But I see no trend towards the quagga regarding the neck and facial stripes. And it brings us to an empirical problem: when is the breeding program progressed enough to say: “ok, this and that trait have not been achieved”? The predictions made have to be falsifiable, otherwise they are of no empiric value. No such timeline has been given, and apart from that, how stable have the characteristics to be in a “recreated quagga population”?

So my conclusion is: Their claim that the quagga was merely a colour variant of “the” plains zebra is likely to be erroneous, their assumption on the genetic background of the stripe pattern is speculative, their guideline that one subspecies can be turned into another by selective breeding on external traits is simplified and probably wrong as my examples have shown, the resemblance of their current results to the quagga are not satisfying yet (contrary to what the QP says) and the resemblance to the quagga is only limitedly falsifiable following their concept.

Perhaps the reason for them considering their results recreated quaggas is just for public relations, but I fear that it is the same kind of self-delusion as it was the case with the Heck brothers. They officially call them Rau quaggas to appreciate that there “might” have been further differences, just as some people call Heck cattle a “model” of the aurochs. But this is not legitimate in my view: There can be no man-made alternative versions of wild animals by definition. Heck cattle is not a model of true wild-type aurochs (not more than any domestic cattle breed is), and the zebras of the QP are not more of a quagga than other Burchell’s zebras are, despite some resemblance in the coat pattern.

This is why I call those zebras “Rau zebras” instead of “Rau quaggas”, as you might have already noticed.




Mammoth DNA inserted into elephant cells, and function normally

The tempting idea of cloning a woolly mammoth, Mammuthus primigenius, inspired by some exceptionally well preserved specimens in the arctic permafrost, is always causing a lot of media attention. Rumors are making the round, of alleged break-throughs, claims that it is all a hoax and scientists that are either very confident or very skeptical on cloning this magnificant and iconic elephant that was no more ancient than the extant three species.

Several ways have been proposed on how it could be done. For example, inseminating an Asian elephant cow with a reconstructed mammoth sperm and subsequent absorptive breeding. A more effective and modern idea is the CRISPR method that is favourised by a number of scientists today. To put it simply, CRISPR is about cutting (splicing) a DNA strand (in this case, an Asian elephant's) at the loci where it differs from the template (mammoth) and to exchange the original base pairs with the ancient ones to create an ever increasingly mammoth-like functional DNA strand. 
Renomed geneticist George M. Church and his lab at the Harvard University are involved in a project that tries to genetically reconstruct a mammoth on long-term sight this way. Now they managed to splice ancient mammoth genes into the genome of an Asian elephant and the ancient genes did indeed show normal function in the A. elephant cells. Allegedly these genes are involved in typical mammoth characteristics, such as subcutaneous fat, small ears and hair growth, but I don't know how reliable that claim is. The results have not been published in a peer-reviewed paper yet because there is more work to do, Church says.


Something similar has already been achieved with a gene of the Thylacine responsible for cartilage formation. Go here for the paper.

Does this bring us closer to seeing a living woolly mammoth again? Not necessarily. But at least it has been shown that it is possible to insert some mammoth genes into the genome of an extant elephant and to have them working normally. Of course it will be possible to create a full mammoth genome this way, as long it is fully resolved, but there are still practical issues, such as using a female elephant as a surrogate and perhaps also epigenetics. We have to be patient. 

Further read: 
http://www.telegraph.co.uk/news/science/science-news/11488404/Woolly-mammoth-could-roam-again-as-extinct-DNA-merged-with-elephant.html
http://www.iflscience.com/plants-and-animals/scientists-successfully-insert-woolly-mammoth-dna-elephant-genome
http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells
http://www.popsci.com/scitech/article/2009-06/shark-factory

For more article on cloning extinct animals, go here: 

Sunday, 8 March 2015

Cloning as a chance for the Wisent


As everybody should know, the extremely low diversity of the contemporary gene pool of the Wisent after the severe bottleneck event during the 1920s and 30s is the most immediate danger for the species’ long-term existence. In this post I outlined how the high degree of inbreeding affects the health and fertility of the global population. I proposed careful, controlled introgression of the American bison as a probable way to add more genetic diversity and resistance to diseases without affecting looks, behaviour and ecology of the Wisent too much, documented in an own breeding book.



When writing my post on extinct species that might one day be revived throughcloning, I came up with another idea helping the Wisent to get out of its genetic misère.   

A well-preserved bone from the early Holocene made it possible to fully sequence the genome of a 9,000 years old aurochs bull. If this is possible, it must be feasible to do the same with the genome of an ancient Wisent. There must be plenty of well-preserved Wisent bones or even soft tissues from early Holocene to the 19th century onwards. Turf remains for example. Even more promising might be remains from historic times, such as hunting trophies in form of skulls and skins.

Once a full genome is recovered, either a complete set of chromosomes could be reconstructed (for which, as far as I know, the technique has not been developed yet), or the genome of a living Wisent could be used as a template and edited according to the ancient nucleotide sequence by genome editing. The latter method should be easier and more feasible. I think that there is a good chance to recover the whole genome of not only one but several ancient Wisents. Acquiring a surrogate would be no problem of course. Any specimen that lived prior to the bottleneck event would be a precious gain of diversity, and five individuals or so might even multiply it. You might be wondering how a small group of Wisent should distribute their genetic material on the whole global population. But one and the same individual can be cloned several times. Cloning as many as possible individuals, both bulls and cows, and adding them to herds in various regions. But adding only bulls, or replacing as much inbreed bulls with cloned bulls as possible would not be ideal in my opinion. The Y types of the cloned individuals have to be added to the population, but should not replace the old ones.



One of the advantages of cloning pre-bottleneck Wisents over the cloning of extinct species is that people won’t raise those annoying “ethical” non-issues and they will see the good in it more immediately than in cloning aurochs, Quagga and so on.

Even better: if it succeeds, those cloned wisents could serve as flagships for the good in cloning ancient animals that might help to get public acceptance.



Maybe the idea of cloning “ancient” wisent as a genetic long-term solution for the conservation of the wisent sounds unconventional. And yes, I am fully aware of the fact that it would face the same general problems of cloning just as any other project does (although, as far as my knowledge does, the offspring of cloned ancient wisents and modern ones would have the developmental problems clones have to a much lesser extent). But if we are honest, this concept is the only way to considerably increase the genetic diversity of the Wisent and therefore to solve its major threat as a species, without affecting its genetic integrity by crossing-in another species.

If you agree with me, feel free to spread this idea. I really hope that people who have the right connections are going to see this and maybe such a project might be realized in near future.

Newborn calves at Faia Brava, Portugal

Faia Brava is a reserve in Portugal that houses one of the two Iberian Tauros cattle herds. So far, this herd is composed of rather nice-looking Maronesa cows and two Sayaguesa bulls that have been added last year. Now, a few newborn calves have been spotted. It is unclear whether the Sayaguesa bulls are the fathers of the new Tauros cattle yet. 
Go here for the article on Rewilding Europe.
The Maronesa cows have a good build and the horns are ok as well, but their colour is pretty dark. I think that they will have to add a breed that contributes a more definite sexual dichromatism in the future, and they might also need more horn thickness. I don't know how large the bulls and cows are, but I estimate the cross bulls might reach a size of 150 cm or so, but this is just a wild guess.

Wednesday, 4 March 2015

Please stop the "Nazi cow" nonsense; and the actual motivation behind the Heck's experiments


You must be warned, this post might get a little bit emotional on some passages.

Of all the myths surrounding Heck cattle, this one is perhaps the most repelling. It states that the idea and attempt to rebreed the aurochs is a product of a national socialist Germanic cult and that the Heck brothers themselves were Nazis and therefore their Heck cattle are “Nazi cows”.
I know that especially in the English speaking world everything that has to do with the national socialists is entertaining, especially when it is something as grotesque as “Nazi cows”. But try not to turn the facts, make up stories, or claim things that are simply not true. What is purported in forums, on blogs, sometimes on Wikipedia and that god-awful NatGeo “documentary” concerning "nazi cows" is simply not true.  
In this post I am going to cover the relationship of the Heck brothers to the national socialist regime and what their true motives of their breeding-back attempts were.

Were the Heck brothers Nazis?

I don’t have statements of neither the Heck brothers themselves nor their relatives at hand that might give a clue on that question, so this paragraph is based solely on extrapolations that I did based on what I know about their biography.

Lutz Heck is the older one of the two. It is a fact that he was a supporting member (Förderndes Mitglied) of the SS from 1933 onwards, the first year of Adolf Hitler’s reign, and joined the NSDAP in 1937. While many heads of German organisations, institutions, companies and so on were members of the NS party, simply out of opportunism, his supporting membership of the SS right from the beginning could be suspicious. Herman Göring was interested in Lutz’s work because he was a fanatic hunter and the idea of hunting big game like the Wisent or a reconstructed aurochs was very appealing to him. Every hunter is keen on hunting big game, and on the other hand, it met Göring’s Germanic fanaticism because these species were native and prey of the ancient Germanic peoples. This fanaticism went to quite a ridiculous extent: sometimes he put on a bear’s coat and stabbed captured deer with wooden spears, “just like the Germanics”, as he believed. Seemingly Göring also interpreted the selective breeding scheme as an analogue to social Darwinism, eliminating the “weak” (in this case domestic) and enforcing the “strong” (wild-type here). Of course this was very comfortable to Heck, because his breeding programs were expensive and needed a lot of space. He would have been a fool not to seize the chance to have a mighty lunatic on his side that would provide him with what he needed. I doubt that Heck, as a zoologist, was prone of such a ridiculous cult around animals, and I cannot imagine that he was that uneducated to share Göring’s idea of breeding-back as an analogue to social Darwinism. All he had to do is to sing along and to lick Göring’s brown boots. The fact that Lutz also created a “German section” in his zoo in Berlin, showing only native animals and ornamenting some of the signs with little swastikas was probably a kind of attraction. I guess that he was particularly interested in European game, it is apparent from his breeding programs, and showing these native species together might also have been inspired by the geo-zoo concept of his brother (placing the paddocks of animals from the same region next to each other). Although it might be morally questionable that Lutz bred with Polish rural horses that were “forcedly sold” to the Germans for his purposes, it certainly was scientific pragmatism. He seized what he could get. Furthermore, it would be ridiculous to claim that the fact that he introduced a few small herds of Heck cattle into game parks of East Prussia and occupied areas of Poland is a sign of German imperialism. He simply wanted to restore an extinct species on its former range, and considered his cattle and his relationship to Göring to be the tool for that.

All in all, I would say that Lutz Heck’s work as director of the Berlin zoo does not suggest that his relationship to the NS ideology and Göring was more than a pragmatic one. However, his supporting membership of the SS indicates a kind of sympathy to me. But I think that calling him Nazi is too much and – not to forget – a massive accusation. 

As to his brother Heinz, it is important to note that he never joined the NSDAP as so many men in leading positions did. In fact, he was one of the only two zoo directors in the German Empire that had never been members of the NS party. He also refused to accept a professor title, what clearly suggests an opposition to the regime. Heinz had, as far as I know, never been in contact with Göring or any other NS official. While the relationship of his brother with the regime and ideology probably was a mix of opportunism and sympathy, I see no sign that one of both was the case in Heinz Heck.

What was the true motivation behind the breeding-back experiments?

The idea to rebreed the aurochs was born in the early 1920s. That alone must give you a clue that no Germanic cult could have been the ideological background for this idea. Fanatic Deutschtum (the cult around the German nation and “Germanic race”) was restricted to nationalistic circles back this time, and only the most radical amongst these would have been that straightforward to integrate cattle into German nationalism.

Actually, it was the fact that their father, Ludwig Heck, had created an extensive collection of cattle breeds at the Berlin Zoo that made his sons realize that some breeds preserve more aurochs traits than others. Heinz Heck made an analogue to domestic budgerigars, which also preserve all traits of their wild type but split up among various newly developed types. Also, it inspired Heinz Heck that a chaotic bunch of domestic rabbits with all kinds of shapes and colours evolved into something that is virtually identical to their wild type when they ran loose in central Europe. He therefore suggested that the same selection on wildtype traits done by nature could be executed by humans and therefore create a look-alike of the aurochs.

This idea had two main motivations: 1) to reconstruct a species that was exterminated by man, and therefore to “correct a mistake”, 2) to show what an aurochs looked like and to point to the fact that the aurochs existed as a species different to the Wisent, with which it was often confused.

Heinz Heck writes:

Due to the lack of the living animal, the aurochs became slowly forgotten, and constantly confused with the wisent […]. So there was the idea of breeding a kind of cattle that looks exactly like its wild predecessor, the aurochs, to rescue it from oblivion.”

Another reason is the idea that, if man cannot be hindered from raging that insanely against himself and all creatures and killing off species after species, it is a very enjoyable fact if one of those species he had already killed off, became resurrected.”

I translated this from Frisch’s 2010 Der Auerochs – das Europäische Rind.

So the motivations behind their rebreeding experiments were solely scientific curiosity, educational and an attempt of species reconstitution. There is not the slightest hint that they did this out of a “Germanic animal cult”.

Also it is not true that Göring himself ordered these breeding attempts. The Heck brothers did it on their own, and Göring was not in any politic position back in the 1920s. I don’t know how Göring came to know about their experiments, but he certainly was the only NS official that knew and cared about it. Adolf Hitler himself probably never heard of that, and even if so, he would not have cared about that. I am not even sure if this man ever visited a zoo or joined a hunt. And it is also a fact that Göring was an eccentric, often to such an extent that he was ridiculed in NS circles. Like when he hunted dressed in a bear’s coat (see above), or his exaggerated uniforms. There is an anecdote that Göring joined a supper dressed in a uniform ornamented with a lot of guns and sabres, and suddenly his belt with all the guns fell of. Hitler was amused and said “Well, as long as he likes it…”.

So the truth behind all that is that two zoo directors did a zoological experiment out of curiosity and passion that coincidentally awoke the interest of one eccentric NS official who was a fanatic hunter. This was convenient for Lutz at least, because their projects were expensive and needed space. Any connection between the attempt at rebreeding the aurochs and the national socialist Germanic cult is baseless. Calling any of the Heck brothers “Nazis” is an unfair accusation (at least for Heinz), and if I personally were a relative of one of the two, I would sue anyone who claims such things.

And how does it fit the Nazi myth that the brothers also tried to rebreed their conception of the “Tarpan”, which they also believed to have inhabited the Russian steppes, or that Lutz Heck also suggested to rebreed the Quagga from living plains zebras, which is certainly not an “ancient Germanic animal”?

To put it in a nutshell: Before you claim or believe such a grotesque story like that, do your history homework. Thanks.

And to the makers of that god-awful NatGeo-documentary, any talentless muckraker of any tabloid purporting that nonsense and anybody who copied it onto Wikipedia and forums to spread it: Shame on you. Yes, shame on you. I hope you guys read that.

Sunday, 1 March 2015

Feral pigs: a correction

A while ago in my dedomestication series, I wrote that the feral pigs in the South of the USA are a good example for a regression towards the wild type through natural selection.

"Although not identical, they bear a considerable resemblance to wild boars in looks, behaviour and movement. They have a body build for agility and strength, and that's how they move. Their tusks are well-pronounced as they have a social and defensive function. The skull is very elongated, as much as in the wild boar – perhaps this is an example of a “reversal” of paedomorphism as described above through developmental cascades [UPDATE: I was pointed out to a paper that suggests that the elongated snout of feral pigs is a result of phenotypic plasticity due to the chewing mechanism]. What is also striking is their (with a few exceptions) uniform fur colour, beautiful mud-coloured brown or very dark, almost black, brown (not as greyish as in the European wild boar) – very likely camouflage in forested environment."

However, Markus Bühler from the Bestiarium provided me with additional facts that force me to revise my statements a bit. 

The fact that those feral pigs resemble wild boar is actually less surprising when considering which kind of farm pigs they descend. Pigs of former centuries cannot simply be equalled with the typical farm pigs of modern times, because they were less productive, less paedomorph, and overall less derived. Some of these populations even descend from those of early Spanish settlers which brought their pigs from the Iberian peninsular, and as everybody who reads this blog will know that Iberia is a hotspot for primitive landraces today. 
So hypothesizing that the wild boar-like apparence of these feral pigs in the South of the USA is mainly due to dedomestication is like claiming the same for an aurochs-like population of feral cattle descending from primitive cattle landraces. Apart from that, these pigs are not as homogeneously coloured as the videos on youtube suggest. In fact, there is stil a variety of colours present in their gene pool.

Therefore, the dedomestication concept, as logical as it is, looses another empirical example.