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:

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.

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.