Thursday, 19 January 2023

Extinct megafauna that could be revived using genome editing

Humans wiped out countless species of animals. Some of those species, particularly those that died out comparably recently, might actually be retrievable. Usually, cloning comes to mind when talking about reviving extinct animals. However, somatic nucleus transfer for reproductive cloning requires an intact cell and not just the DNA of the animal, which is why it is not available for most species wiped out by man. However, there are a few megafaunal species that have been wiped off from which we have at least one and in some cases several complete genomes. If there is a still extant species that is closely related and would make a suitable surrogate, it would be possible to exchange the alleles specific for species A with those for species B and thus creating a viable cell with the genome of the extinct species in question with genome editing. This limits the number of extinct animals that could be revived. For example, I would imagine it to be pretty difficult if not impossible for a species like the thylacine, which has been evolutionary separated for 30 million years from its closest living relatives. In some cases, it could be easy and much less effortful because of the lower number of genes that differ and the suitability of the surrogate because the animal has a very close living relative. In this post, I present a number of megafaunal species from which full genomes either have been acquired or at least could potentially be acquired and which have a more or less closely related relative that can be used for genome editing and as a surrogate. The mitochondrial DNA of the resulting animal would be that of the donor cell, which would be from the related species. However, as mitochondrial genes are highly conserved among mammals this would not have much of an influence. Using closely related species also has the advantage that the behaviour will be rather similar, especially among the large herbivore species that I am going to list. This makes the rearing by a surrogate mother and socialization of the result less problematic or maybe not even an issue at all. 

I see reviving an extinct animal that has been wiped out by man as a contribution to species conservation just as breeding an endangered species or subspecies. One might ask, particularly in the case of wiped-out subspecies, why doing that at all if there are suitable ecological proxies. Occasionally some even question the need to conserve endangered subspecies such as the Northern White rhino because their conspecifics from other subspecies would function ecologically the same or very similar. Personally, I cannot relate to that mindset. Conservation is about preserving biodiversity and the preservation of evolutionary more or less distinct subspecies is a vital part of that. The same goes for reviving extinct species or subspecies – it would greatly increase the biodiversity again, after it has been depleted by man when the species or subspecies was wiped out. 

 

Bubal hartebeest, Alcelaphus buselaphus  

This animal is sometimes also considered a subspecies, but that question is merely taxonomical and not relevant for “de-extincting” the animal. In any case, other members of Alcelaphus could be used for genome editing and as a surrogate. Many individuals must have been preserved as trophies, and it is potentially possible to acquire full nuclear genomes from them. 

 

Bluebuck, Hippotragus leucophaeus  

Other members of Hippotragus could be used as a surrogate and for genome editing. It can be tried to acquire a fully nuclear genome from taxidermies.  

 

European aurochs, Bos primigenius primigenius

One full nuclear genome has been resolved in 2015 from a well-preserved Neolithic bone. Considering the richness of recent aurochs material, it could be possible to obtain quite a few more complete genomes. And there is a very close living relative, modern cattle. The number of genes that would have to be exchanged would probably be lower than in most of the other cases I am listing here, and also the surrogate and the procedure of implanting an embryo would be completely unproblematic. And considering the similarities in behaviour between cattle and aurochs, socialization will not be problematic either. For these reasons, I consider the aurochs one of the most realistic candidates for a revival through genome editing. Even if the resolved genome remains the only one to be fully resolved, one revived aurochs individual still can be outbred using aurochs-like cattle. I wrote a post on that a few years ago. 

 

Several types of wild horses 

There are well-preserved mummies of Siberian wild horses, Equus caballus lenensis, and one of the Yukon wild horse, Equus caballus lambei, so it could be possible to obtain fully resolved nuclear genomes from that. A domestic horse could be used for genome editing and as a surrogate. Even if only one genome can be obtained, the revived horses can be outbred with Przewalski’s horses and/or robust landraces in the same manner as I suggested for revived aurochs. 

 

Kouprey, Bos sauveli  

Numerous kouprey specimen have been preserved as trophies and one skin. It could be possible to obtain full nuclear genomes from that very recent material. The closest living relative is the Cambodian banteng which hybridized with the kouprey in the past. It can be used for genome editing, as a surrogate and even for outbreeding if necessary. 

 

Quagga, Equus quagga quagga  

The quagga is not and cannot be bred-back from extinction with living Plains zebras, which is why it would be desirable to try to acquire full genomes from the numerous preserved skins and the few skeletal material that is preserved of this zebra. The zebras of the Quagga Project can be used for genome editing, as a surrogate and outbreeding if necessary. 

 

Pyrenean ibex, Capra pyrenaica pyrenaica  

This is the only extinct animal that has been cloned so far, unfortunately the clone died shortly after birth. Genome editing with individuals from other subspecies of Capra pyrenaica could be more successful, they can be used as surrogates and for outbreeding. 

 

Steppe bison, Bos (Bison) priscus  

There are plentiful of remains from steppe bison, including soft tissue. Perhaps it would be possible to obtain full nuclear genomes from that. Needless to say, that still existing bison, be it European or American, can be used for genome editing, as a surrogate and outbreeding. 

 

? Woolly mammoth, Mammuthus primigenius  

Currently, there is no de-extinction project in the strict sense focusing on the woolly mammoth. There is the attempt to create a “mammophant” by introducing mammoth alleles for certain traits into the genome of an Asian elephant, what is not what I would consider de-extinction in the strict sense. If doing that is possible, it might also be possible even if more effortful, to exchange all alleles of genes where Asian elephant and woolly mammoth differ. However, since implanting an embryo into an elephant is very complicated, and those who want to create plan to use an artificial womb, a technique which does not exist hitherto, I wonder if it is feasible to recreate the woolly mammoth for practical reasons. 

 

Caucasian Wisent, Bos (Bison) bonasus caucasicus  

Several skins and trophies of this wiped-out subspecies (or species or variety, there is no consensus on its taxonomic status) exist, so it could be possible to obtain full nuclear genomes from it. European bison of the Lowland-Caucasus line, which partly descend from the last Caucasian wisent bull, could be used for genome editing, as a surrogate and for outbreeding. Obtaining genomes from remains of wisent prior to the bottleneck in the 20th century could also help to greatly increase the very limited genetic diversity of this endangered bovine. 

 

Cave lion, Panthera spelaea  

Several very well-preserved pubs of this feline have been found. It might be possible to acquire full nuclear genomes from that, and the closely related actual lion would be suitable for genome editing and as a surrogate. 

 

Schomburgk’s deer, Rucervus schomburgki  

Some remains of this deer species exist, a sister species from the Rucervus clade could be used for genome editing and as a surrogate. 

 

Japanese sea lion, Zalophus japonicus

There are taxidermied specimens of this sea lion, related species of the Zalophus clade can be used for genome editing, as a surrogate and possibly outbreeding if necessary. 

 

Caribbean monk seal, Neomonachus tropicalis

There should be some remains of this recently extinct species, the related Hawaiian monk seal can be used for genome editing, as a surrogate and possibly outbreeding if necessary. 

 

One common objection against the revival of extinct animals is “one individual is not enough to build a population”. Apart from the fact that even one individual could tell us a lot about the extinct animal species/subspecies, it could be possible to get several genomes of those recently extinct species. Getting the full genome of five or ten individuals from different regions and times would probably enable to get a genetic diversity comparable to that of the modern wisent population, which descends from only twelve founding individuals from the same population. Some wisent individuals show inbreeding-related problems, but not to the extent that it threatens the survival of the species. An even more extreme example would be the Mauritius kestrel. Apart from that, related species/subspecies can always be used for outbreeding to add genetic diversity. Hybridization among related species with neighboring or overlapping distributions is very common in the animal kingdom. 

 

2 comments:

  1. Worth noting that 2-3 Equus caballus lambei genomes already exist. I would argue that in the case of the Bubal hartebeest, it would be more expedient and equally effective to rewild other subspecies in the North African range. Rewilding of other Capra pyrenaica subspecies in the French Pyrenees has already begun. The current mammoth projects plan to use artificial womb technology, which is rapidly progressing, in order to dispense with using elephant surrogates at all. I also think that rewilding barasingha, California sea lion, and Hawaiian monk seal in the ranges of their sister species would be a better use of resources than de-extinction. The utility of cave lion and steppe/European bison DNA would probably be more in augmenting existing genomes than in synthesizing new ones, as with mammoths and horses.

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  2. Actually, you should not really need multiple genomes when de-extincting species via genome editing. Once you have one genome, you 'just' need to identify all heterozygous mutations that would be pathogenic if homozygous and then not introduce those. There is nothing intrinsically good about variation (aside of certain immune traits or maybe size differences that decrease competition within the population) and inbred lines exist for different species like mice or guppys. Of course, an inbreed population is slightly slower to adapt to difference in conditions (as mentioned above). However, the de-facto main reason why you do not want inbreeding is because it increases the chance of getting rare loss of function mutations on both haplotypes and if you eliminate those I do not see a reason to start a population with (male and female) clones.

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