Przewalski's horse cloned for genetic diversity

In 2015 I proposed cloning as a chance for the wisent's survival. Cloning pre-bottleneck wisents would greatly increase the genetic diversity of the species, since the modern population descends from a population of only about 50 individuals which itself descended from only 12 individuals. Adding the genetic diversity of wisents that lived before the dramatic bottleneck event in the 20th century would help the species to overcome its inbreeding depression. And if cloning is not possible, genome editing with CRISPR-Cas9 is a viable alternative. 

It seems that there are people who had the same idea for the Przewalski's horse, which descends from only 12 individuals as well. A stallion has been cloned from an individual that has been cryopreserved since 1980. For details, you can have a look at the article from Revive & Restore. 

I hope that cloning for conservation will not be restricted to this one individual. I hope this idea will be put into practice for other species as well, including the wisent. 

Complete genome of two woolly mammoths sequenced

Mammoth DNA made it into the news again. Until recently, the genome of Mammuthus primigenius was not completely resolved yet, but now it is - not only of one individual, but actually two. These two individuals, both males and from Siberia, lived about 40.000 years apart from each other. The older one is from approx. 44,800 years ago, late Pleistocene, and the other one 4,300 years ago. The younger one lived on Wrangel Island, the last refuge of the Woolly Mammoth, back the time when the ancient Egyptians built their pyramids (which is a fascinating thought to me). 
The study, published by Palkopoulou et al.[1] in Current Biology, revealed interesting but not surprising facts. The population of the Eurasian woolly mammoth went through a considerable bottleneck during the middle Pleistocene, which is consistent with the fact that their habitat had shrunken dramatically back this time due to the interglacial climate [2]. The same happened at the early Holocene of course, but still mammoths survived into the antiquary. The last refugee population on Wrangel had a rather small genetic diversity, and likely also suffered from an inbreeding depression, which is confirmed by this study. Undoubtedly it was a mix of several factors that drove the last mammoths to extinction, but I think it is likely that man played a considerable role in it. In my opinion, perhaps not the vulnerable Wrangel population but at least the core population in the North Siberian tundra might have survived without any human hunting pressure. 

[1] Palkopoulou et al.: "Complete genomes reveal signatures of demographic declines in the Woolly Mammoth", Current Biology 2015.
[2] Nogues-Bravo et al.: "Climate change, humans, and the extinction of the Woolly Mammoth", PLOS Biology, 2008.

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: 

• Clong as a chance for the Wisent? 
• Extinct species/subspecies that could be revived through cloning 
• Complete genome of an aurochs sequenced 

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 19^th 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.

Complete Genome of an Aurochs sequenced! Finally!

A paper presenting the fully-resolved nuclear genome of an aurochs individual from Britain is finally about to get published. They used an exceptionally well-preserved humerus from about 7.000 years BP.  Here you have the abstract: 

"The extinct wild Eurasian aurochs (Bos primigenius) was the progenitor of domestic taurine cattle (B. taurus). Although genetic and archaeological studies pinpoint the Near East as the centre of origin for Bos taurus, recent genetic evidence suggests that historical admixture may have occurred between domestic taurine cattle and wild aurochsen. Here, we present analyses of the first complete nuclear genome from an archaeologically-verified and exceptionally well-preserved aurochs humerus bone sample recovered from a cave site in Derbyshire, England and radiocarbon-dated to 6,738 ± 68 calibrated years before present (laboratory sample code: CPC98). Previous work in our laboratory has shown that this aurochs possessed a haplogroup P mitochondrial sequence, which predominates in Northern European aurochs samples examined to-date. For the present study, DNA extracts from the CPC98 humerus bone were prepared for Illumina^® short read, high-throughput DNA sequencing. A consensus CPC98 B. primigenius nuclear genome was assembled, using the complete B. taurus genome. A mean read depth of 6.2× was generated from 470 million reads aligned to unique locations in the template genome, yielding a genome coverage of 2.37 Gb. Phylogenetic analyses using Illumina^® BovineSNP50 BeadChip genotype data from modern B. taurus and B. indicus cattle place the CPC98 sample as an outgroup to all modern taurine cattle, consistent with common ancestry of taurine cattle from Near-Eastern aurochs. We have performed comparative analyses of coding sequences or candidate regulatory regions associated with genes using high-throughput DNA sequencing data from modern B. taurus and B. indicus cattle to identify over 300 genes in which CPC98 and indicine cattle share potentially functional SNP or indel alleles not seen in taurine cattle. Selection at these genes throughout the history of domestication and selective breeding may have played a key role in shaping the genome of modern taurine cattle."

Before you get too euphoric, this individual cannot be cloned yet. It is a reconstructed sequence, for cloning this aurochs you need a functioning set of chromosomes. One method to reconstruct this individual using the genome is to modify the genome of a domestic cattle step-by-step to achieve a 100% aurochs, but this is a long-term process. Another possibility is de novo synthesis of the chromosome set, which is technically not possible yet but might be in the near future. 

Nevertheless, this is more-ground braking than it sounds at first. The fact that it was possible to sequence the full genome from this early Holocene bone might indicate that this is possible with a large number of individuals - maybe close to 100, based on the large number of aurochs remains that we know. It might not only be possible to do that with the aurochs alone - it might be possible with the Holocene wild horses of Europe as well - and a whole set of other early Holocene and late Pleistocene extinct species. And if the gained genetic diversity to low, it can always be improved by crossing-in similar domestic counterparts. We know that these species serve a function in the european ecosystems and that they were exterminated by man, so the answer to the question "Should be do this?" is "yes, definitely we should". And even if the animals don't serve a function in modern ecosystems like saber-toothed cats, it's still a huge progress in studying these animals, so it is desirable in any case. The "ethical problems" related to genetic reconstructions provoked by people who have hardly an idea what they are talking about are quite a non-issue, so let's not concern us with that. 

Although technique is not ready yet, the possibility is good that we see several true aurochs in flesh again in a not too distant future!