De-extinction

Pictured above is the process used to clone the Pyrenean ibex in 2003. The tissue culture was taken from the last living, female Pyrenean ibex named Celia. The egg was taken from a goat (Capra hircus) and the nuclei removed to ensure the offspring was purely Pyrenean ibex. The egg was implanted into a surrogate goat mother for development.

Cloning is a commonly suggested method for possible restoration of an extinct species. This can be done by extracting the nucleus from a preserved cell from the extinct species and swapping it into an egg, without a nucleus, of the nearest living relative.[3] This egg can then be inserted into a relative host. It is important to note that this method can only be used when a preserved cell is available. This means, this would be most feasible for recently extinct species.[4] Cloning has been used in science for years and dates back to the 1950s.[5] One of the most well known, successful clones is Dolly, the sheep. Dolly was born in the mid 1990s and lived a normal life until she had health complications, eventually leading to her death.[5] Sheep are not the only species to undergo cloning. Some common species include dogs, pigs, and horses.[5]

Genome editing has been rapidly advancing with the help of the CRISPR/Cas systems, particularly CRISPR/Cas9. The CRISPR/Cas9 system was originally discovered as part of the bacterial immune system.[6] Viral DNA that was injected into the bacterium became incorporated into the bacterial chromosome at specific regions. These regions are called clustered regularly interspaced short palindromic repeats, otherwise known as CRISPR. Since the viral DNA is within the chromosome, it gets transcribed into RNA. Once this occurs, the Cas9 binds to the RNA. Cas9 can recognize the foreign insert and cleaves it.[6] This discovery was very crucial because now the Cas protein can be viewed as a scissor in the genome editing process.

By using cells from a closely related species to the extinct species, genome editing can play a role in the de-extinction process. Germ cells may be edited directly, so that the egg and sperm produced by the extant parent species will produce offspring of the extinct species, or somatic cells may be edited and transferred via somatic cell nuclear transfer. This results in a hybrid between the two species, since it is not completely one animal. Because it is possible to sequence and assemble the genome of extinct organisms from highly degraded tissues, this technique enables scientists to pursue de-extinction in a wider array of species, including those for which no well-preserved remains exist.[3] However, the more degraded and old the tissue from the extinct species is, the more fragmented the resulting DNA will be, making genome assembly more challenging.

Back breeding is a form of selective breeding. As opposed to breeding animals for a trait to advance the species in selective breeding, back breeding involves breeding animals for an ancestral characteristic that may not be seen throughout the species as frequently.[7] This method can recreate the traits of an extinct species, but the genome will differ from the original species.[4] Back breeding, however, is contingent on the ancestral trait of the species still being in the population in any frequency.[7]

A natural process of de-extinction is iterative evolution. This process occurs when a species becomes extinct, but then reappears after some amount of time. An example of this process occurred with the white-throated rail. This flightless bird became extinct approximately 136,000 years ago due to an unknown event that caused sea levels to rise, which resulted in the demise of the species. The species reappeared about 100,000 years ago when sea levels dropped, allowing the bird to evolve once again as a flightless species on the island of Aldabra, where it is found to the present day.[8][9][10] Also see Elvis taxon.

The existence of preserved soft tissue remains and DNA of woolly mammoths has led to the idea that the species could be recreated by scientific means. Two methods have been proposed to achieve this. The first would be to use the cloning process. This is proposed because even the most intact mammoths have had little usable DNA because of their conditions of preservation. There is not enough to guide the production of an embryo.[13] The second method involves artificially inseminating an elephant egg cell with preserved sperm of the mammoth. The resulting offspring would be an elephant–mammoth hybrid. After several generations of cross-breeding these hybrids, an almost pure woolly mammoth would be produced. However, sperm cells of modern mammals are potent for 15 years at most after deep-freezing, which provides a hindrance to this method.[14] In 2008, a Japanese team found usable DNA in the brains of mice that had been frozen for 16 years. They hope to use similar methods to find usable mammoth DNA.[15] In 2011, Japanese scientists announced plans to clone mammoths within six years.[16] As the woolly mammoth genome has been mapped, complete chromosomal DNA molecules may be synthesized in the future.[17]

It was reported in March 2014 that blood recovered from a frozen mammoth carcass in 2013 now provides a better opportunity for cloning the woolly mammoth, despite previous hindrances.[14] Another way to revive the woolly mammoth would be to migrate genes from the mammoth genome into the genes of its closest living relative, the Asian elephant, to create hybridized animals with the notable adaptations that it had for living in a much colder environment than modern day elephants. This is currently being done by Harvard geneticist George Church. They have already successfully made changes in the elephant genome with the genes that gave the woolly mammoth its cold-resistant blood, longer hair, and extra layer of fat.[18] A revived woolly mammoth or mammoth-elephant hybrid may find suitable habitat in the tundra and taiga forest ecozones.[19]

George Church gives an example of the positive effects of bringing back the extinct woolly mammoth would have on the environment. He explains that if the newly developed mammoth hybrids were to be placed in areas such as Siberia and Alaska, the outcome may reverse the damage that global warming has caused.[20] He and his fellow researchers predict that mammoths would eat the dead grass allowing the sun to reach the spring grass; their weight would allow them to break through dense, insulating snow in order to let cold air reach the soil; and their characteristic of felling trees would increase the absorption of sunlight. If the theories are proven true, global warming could eventually be lessened in these areas.[20] Scientific American, in an editorial condemning de-extinction, pointed out that the technologies involved could have secondary applications, specifically to help species on the verge of extinction regain their genetic diversity.

The Pyrenean ibex was one of four original subspecies of Spanish ibex that roamed on the Iberian peninsula. While it was abundant up to the Medieval times, over-hunting in the 19th and 20th centuries led to its demise. In 1999, only a single female named Celia was left alive in Ordesa National Park. Scientists captured her, took a tissue sample from her ear, collared her, then released her back into the wild, where she lived until she was found dead in 2000, having been crushed by a fallen tree. In 2003, scientists used the tissue sample to attempt to clone Celia and resurrect the extinct subspecies. Despite having successfully transferred nuclei from her cells into domestic goat egg cells and impregnating 208 female goats, only one came to term. The baby ibex that was born had a lung defect, and lived for only 7 minutes before suffocating from being incapable of breathing oxygen. Nevertheless, her birth was seen as a triumph and has been considered to have been the first de-extinction.[21] In late 2013, scientists announced that they would again attempt to recreate the Pyrenean ibex. A problem to be faced, in addition to the many challenges of reproduction of a mammal by cloning, is that only females can be produced by cloning the female individual Celia, and no males exist for those females to reproduce with. This could potentially be addressed by breeding female clones with the closely related Southeastern Spanish ibex, and gradually creating a hybrid animal that will eventually bear more resemblance to the Pyrenean ibex than the Southeastern Spanish ibex.[22]

The Auroch size compared to the size of a human.

The aurochs was widespread across Eurasia, North Africa, and the Indian subcontinent during the Pleistocene, but only the European aurochs (Bos primigenius primigenius) survived into historic times.[23] This species is heavily featured in European cave paintings, such as Lascaux and Chauvet cave in France,[24] and was still widespread during the Roman era. Following the fall of the Roman empire, overhunting of the aurochs by nobility caused its population to dwindle to a single population in the Jaktorów forest in Poland, where the last wild one died in 1627.[25] However, because the aurochs is ancestral to most modern cattle breeds, it is possible for it to be brought back through selective or back breeding. The first attempt at this was by Heinz and Lutz Heck using modern cattle breeds, which resulted in the creation of Heck cattle. This breed has been introduced to nature preserves across Europe; however, it differs strongly from the aurochs in both physical characteristics and behavior, and modern attempts have tried to create an animal that is nearly identical to the aurochs in morphology, behavior, and even genetics.[26] The TaurOs Project aims to recreate the aurochs through selectively breeding primitive cattle breeds over a course of twenty years to create a self-sufficient bovine grazer in herds of at least 150 animals in rewilded nature areas across Europe.[27] This organization is partnered with the organization Rewilding Europe to help restore balance to European nature.[28] A competing project to recreate the aurochs is the Uruz Project by the True Nature Foundation, which aims to recreate the aurochs through a more efficient breeding strategy and through genome editing, in order to decrease the number of generations of breeding needed and the ability to quickly eliminate undesired traits from the new aurochs population.[29] It is hoped that the new aurochs will reinvigorate European nature by restoring its ecological role as a keystone species, and bring back biodiversity that disappeared following the decline of European megafauna, as well as helping to bring new economic opportunities related to European wildlife viewing.[30]

The quagga (Equus quagga quagga) is a subspecies of the plains zebra that was distinct in that it was striped on its face and upper torso, but its rear abdomen was a solid brown. It was native to South Africa, but was wiped out in the wild due to overhunting for sport, and the last individual died in 1883 in the Amsterdam Zoo.[31] However, since it is technically the same species as the surviving plains zebra, it has been argued that the quagga could be revived through artificial selection. The Quagga Project aims to recreate the animal through the selective or back breeding of plains zebras.[32] It also aims to release these animals onto the western Cape once an animal that fully resembles the quagga is achieved, which could have the benefit of eradicating non-native trees.[33]

The last known thylacine, named "Benjamin", died from neglect in the Hobart Zoo in 1936.

The thylacine was native to the Australian mainland, Tasmania and New Guinea. It is believed to have become extinct in the 20th century. The thylacine had become extremely rare or extinct on the Australian mainland before British settlement of the continent. The last known thylacine, named Benjamin, died at the Hobart Zoo, on September 7, 1936. It is believed to have died as the result of neglect—locked out of its sheltered sleeping quarters, it was exposed to a rare occurrence of extreme Tasmanian weather: extreme heat during the day and freezing temperatures at night.[34] Official protection of the species by the Tasmanian government was introduced on July 10, 1936, roughly 59 days before the last known specimen died in captivity.[35]

In December 2017 it was announced in Nature Ecology and Evolution that the full nuclear genome of the thylacine had been successfully sequenced, marking the completion of the critical first step toward de-extinction that began in 2008, with the extraction of the DNA samples from the preserved pouch specimen.[36] The Thylacine genome was reconstructed by using the genome editing method. The Tasmanian devil was used as a reference for the assembly of the full nuclear genome.[37] Andrew J. Pask from the University of Melbourne has stated that the next step toward de-extinction will be to create a functional genome, which will require extensive research and development, estimating that a full attempt to resurrect the species may be possible as early as 2027.[36]

Martha, the last known passenger pigeon

The passenger pigeon numbered in the billions before being wiped out due to commercial hunting and habitat loss. The non-profit Revive & Restore obtained DNA from the passenger pigeon from museum specimens and skins; however, this DNA is degraded because it is so old. For this reason, simple cloning would not be an effective way to perform de-extinction for this species because parts of the genome would be missing. Instead, Revive & Restore focuses on identifying mutations in the DNA that would cause a phenotypic difference between the extinct passenger pigeon and its closest living relative the band-tailed pigeon. In doing this, they can determine how to modify the DNA of the band-tailed pigeon to change the traits to mimic the traits of the passenger pigeon. In this sense, the de-extinct passenger pigeon would not be genetically identical to the extinct passenger pigeon, but it would have the same traits. The de-extinct passenger pigeon hybrid is expected to be ready for captive breeding by 2024 and released into the wild by 2030.[38]

• Moa – this group of large (up to 4 m [12 ft] tall and 110 kg [250 lb]), flightless birds became extinct in approximately 1400 AD following the arrival and proliferation of the Maori people on New Zealand; however, intact DNA from both preserved specimens and eggshells makes the moa a candidate for resurrection.[39] New Zealand politician Trevor Mallard has suggested bringing back a medium-sized species.[40]
• Heath hen – this subspecies of the prairie chicken became extinct on Martha's Vineyard in 1932 despite conservation efforts; however, the availability of usable DNA in museum specimens and protected areas in its former range makes this bird a possible candidate for de-extinction and reintroduction to its former habitat.[41]
• Dodo – this large, flightless ground bird endemic to Mauritius became extinct in the 1640s, less than a century after it was discovered, due to exploitation by humans and due to introduced species such as rats and pigs, which ate their eggs, and has since become a symbol of extinction in popular culture. Due to a wealth of bones and some tissues, it is possible that this species may live again as it has a close relative in the surviving Nicobar pigeon.[42] The entire dodo bird genome has been sequenced, but further steps towards de-extinction have not yet been made.[43]
• Elephant bird – of the largest birds to have ever existed, the elephant bird was driven to extinction by the early colonization of Madagascar. Ancient DNA has been obtained from the eggshells but may be too degraded for use in de-extinction.[44]

• Caribbean monk seal
• Irish elk
• Japanese sea lion
• Cave lion – The discovery of two preserved cubs in the Sakha Republic ignited a project to clone the animal.[45]
• Steppe bison – The discovery of the mummified steppe bison of 9,000 years ago could help people clone the ancient bison species back, even though the steppe bison would not be the first to be "resurrected".[46]
• Tarpan – A subspecies of wild horse that went extinct in 1909. Much like the aurochs, there have been many attempts to breed tarpan-like horses, the first being by the Heck brothers, creating the Heck horse as a result. Though it is not a genetic copy, it is claimed to bear many similarities to the tarpan.[47] Other attempts were made to create tarpan-like horses. A breeder named Harry Hegardt was able to breed a line of horses from American Mustangs.[48] Other breeds of tarpan-like horse include the Konik and Strobel's horse.
• Woolly rhinoceros – Similar reasons of bringing back as the woolly mammoth.
• Macrauchenia – The DNA of Macrauchenia, which has been discovered in 2017, makes it possible for Macrauchenia to be cloned.[49]
• Neanderthal

• Floreana Island tortoise – In 2008, mitochondrial DNA from the Floreana tortoise species was found in museum specimens. In theory, a breeding programme could be established to "resurrect" a pure Floreana species from living hybrids.[50][51]

• Gastric-brooding frog – In 2013, scientists in Australia successfully created a living embryo from non-living preserved genetic material, and hopes by using somatic-cell nuclear transfer methods, they can produce an embryo that can survive to the tadpole stage.[52]