De-extinction

Pictured above is the process used to clone the Pyrenean ibex. 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 nucleus 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 the potential restoration of an extinct species. It 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 that species' nearest living relative.[3] The egg can then be inserted into a host from the extinct species' nearest living relative. It is important to note that this method can only be used when a preserved cell is available, meaning it would be most feasible for recently extinct species.[4] Cloning has been used by scientists since the 1950s.[5] One of the most well known clones is Dolly the sheep. Dolly was born in the mid 1990s and lived normally until the abrupt midlife onset of health complications resembling premature aging, that led to her death.[5] Other known cloned animal species include domestic cats, 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. The result is an animal which is not completely the extinct species, but rather a hybrid of the extinct species and the closely related, non-extinct species. 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] Back breeding is also a form of artificial selection by the deliberate selective breeding of domestic animals, in an attempt to achieve an animal breed with a phenotype that resembles a wild type ancestor, usually one that has gone extinct. Breeding back is not to be confused with dedomestication.

A natural process of de-extinction is iterative evolution. This occurs when a species becomes extinct, but then after some time a different species evolves into an almost identical creature. For example, the Aldabra rail was a flightless bird that lived on the island of Aldabra. It had evolved some time in the past from the flighted white-throated rail, but became extinct about 136,000 years ago due to an unknown event that caused sea levels to rise. About 100,000 years ago, sea levels dropped and the island reappeared, with no fauna. The white-throated rail recolonized the island, but soon evolved into a flightless species taxonomically identical to the extinct species.[8][9][10]

The existence of preserved soft tissue remains and DNA from woolly mammoths (Mammuthus primigenius) 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, however even the most intact mammoth samples have had little usable DNA because of their conditions of preservation. There is not enough DNA intact to guide the production of an embryo.[18] The second method would involve artificially inseminating an elephant egg cell with preserved sperm of the mammoth. The resulting offspring would be a hybrid of the mammoth and its closest living relative the Asian elephant. After several generations of cross-breeding these hybrids, an almost pure woolly mammoth could be produced. However, sperm cells of modern mammals are typically potent for up to 15 years after deep-freezing, which could hinder this method.[19] 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.[20] In 2011, Japanese scientists announced plans to clone mammoths within six years.[21]

In March 2014, the Russian Association of Medical Anthropologists reported that blood recovered from a frozen mammoth carcass in 2013 would now provide a good opportunity for cloning the woolly mammoth.[19] Another way to create a living 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 a team led by Harvard geneticist George Church.[22] The team has made changes in the elephant genome with the genes that gave the woolly mammoth its cold-resistant blood, longer hair, and an extra layer of fat.[22] According to geneticist Hendrik Poinar, a revived woolly mammoth or mammoth-elephant hybrid may find suitable habitat in the tundra and taiga forest ecozones.[23]

George Church has hypothesized the positive effects of bringing back the extinct woolly mammoth would have on the environment, such as the potential for reversing some of the damage caused by global warming.[24] 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.[24] In an editorial condemning de-extinction, Scientific American pointed out that the technologies involved could have secondary applications, specifically to help species on the verge of extinction regain their genetic diversity.[25]

Taxidermied Pyrenean ibex, MHNT

The Pyrenean ibex (Capra pyrenaica pyrenaica) was a subspecies of Iberian ibex that lived on the Iberian Peninsula. While it was abundant through 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 seven minutes before suffocating from being incapable of breathing oxygen. Nevertheless, her birth was seen as a triumph and is considered the first de-extinction.[26] In late 2013, scientists announced that they would again attempt to resurrect 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.[27]

The aurochs, bull and cow.

The aurochs (Bos primigenius) was widespread across Eurasia, North Africa, and the Indian subcontinent during the Pleistocene, but only the European aurochs (B. p. primigenius) survived into historical times.[28] This species is heavily featured in European cave paintings, such as Lascaux and Chauvet cave in France,[29] 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.[30]

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 physical characteristics, and some modern attempts claim to try to create an animal that is nearly identical to the aurochs in morphology, behavior, and even genetics.[31] There are several projects that aim to create a cattle breed similar to 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, for example the Tauros Programme and the separate Taurus Project.[32] This organization is partnered with the organization Rewilding Europe to help revert some European natural ecosystems to their prehistoric form.[33]

A competing project to recreate the aurochs is the Uruz Project by the True Nature Foundation, which aims to recreate the aurochs by a more efficient breeding strategy using genome editing, in order to decrease the number of generations of breeding needed and the ability to quickly eliminate undesired traits from the population of aurochs-like cattle.[34] It is hoped that aurochs-like cattle 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.[35]

Living quagga, 1870

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.[36] 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 breed a similar form of zebra by selective breeding of plains zebras.[37] This process is also known as back breeding. 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 introduced species of trees such as the Brazilian pepper tree, Tipuana tipu, Acacia saligna, bugweed, camphor tree, stone pine, cluster pine, weeping willow and Acacia mearnsii.[38]

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

The thylacine (Thylacinus cynocephalus), commonly known as the Tasmanian tiger, 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 died at the Hobart Zoo, on September 7, 1936. He is believed to have died as the result of neglect—locked out of his sheltered sleeping quarters, he was exposed to a rare occurrence of extreme Tasmanian weather: extreme heat during the day and freezing temperatures at night.[39] 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.[40]

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.[41] 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.[42] 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.[41]

In August 2022, the University of Melbourne and Colossal Biosciences announced a partnership to accelerate de-extinction of the thylacine via genetic modification of one of its closest living relatives, the fat-tailed dunnart.[43]

Martha, the last known passenger pigeon

The passenger pigeon (Ectopistes migratorius) numbered in the billions before being wiped out due to unsustainable commercial hunting and habitat loss during the early 20th century. 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. In 2015, the de-extinct passenger pigeon hybrid was forecast ready for captive breeding by 2024 and released into the wild by 2030.[44]

Maclear's rat, naturalist's painting.

The Maclear's rat (Rattus macleari), also known as the Christmas Island rat, was a large rat endemic to Christmas Island in the Indian Ocean. It is believed Maclear's rat might have been responsible for keeping the population of Christmas Island red crab in check. It is thought that the accidental introduction of black rats by the Challenger expedition infected the Maclear's rats with a disease (possibly a trypanosome),[45] which resulted in the species' decline.[46] The last recorded sighting was in 1903.[47] In March 2022, researchers discovered the Maclear's rat shared about 95% of its genes with the living brown rat, thus sparking hopes in bringing the species back to life. Although scientists were mostly successful in using CRISPR technology to edit the DNA of the living species to match that of the extinct one, a few key genes were missing, which would mean resurrected rats would not be genetically pure replicas.[48]

• Little bush moa – A slender species of moa slightly larger than a turkey that went extinct abruptly, around 500-600 years ago following the arrival and proliferation of the Māori people in New Zealand, as well as the introduction of Polynesian dogs.[50] Scientists at Harvard University assembled the first nearly complete genome of the species from toe bones, thus bringing the species a step closer to being "resurrected".[51][52] New Zealand politician Trevor Mallard had previously suggested bringing back a medium-sized species of moa.[53]
• 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.[54][55]
• Dodo – This large, flightless ground bird endemic to Mauritius was last sighted in the 1640s and was most likely extinct by 1700, due to exploitation by humans and due to introduced species such as rats and pigs, which ate their eggs. It 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.[56]
• Elephant bird – Some of the largest birds to have ever existed, the elephant birds were 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.[57][58]
• Carolina parakeet - One of the only indigenous parrots to North America, it was driven to extinction by destruction of its habitat, overhunting, competition from introduced honeybees, and persecution for crop damages. Hundreds of specimens with viable DNA still exist in museums around the world, making them a prime candidate for revival.[57][52]
• Great auk - A flightless bird native to the North Atlantic similar to the penguin. The great auk went extinct in the 1800s due to overhunting by humans for food. The last two known great auks lived on an island near Iceland and were clubbed to death by sailors. There have been no known sightings since.[59] The great auk has been identified as a good candidate for de-extinction by Revive and Restore, a non-profit organization. Because the great auk is extinct it cannot be cloned, but its DNA can be used to alter the genome of its closest relative, the razorbill, and breed the hybrids to create a species that will be very similar to the original great auks. The plan is to introduce them back into their original habitat, which they would then share with razorbills and puffins, who are also at risk for extinction. This would help restore the biodiversity and restore that part of the ecosystem.[60]
• Imperial woodpecker[57][52]
• Ivory-billed woodpecker[57][52]
• Cuban macaw[57][52]
• Labrador duck[57][52]
• Huia[57][52]
• Moho[57][52]

• Caspian tiger
• Caribbean monk seal[57][52]
• Irish elk[57][52]
• Cave lion – The discovery of two preserved cubs in the Sakha Republic ignited a project to clone the animal.[61][62]
• 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".[63] Russian and South Korean scientists are collaborating to clone steppe bison in the future, using DNA preserved from a 8,000 year old tail,[64][65] in wood bison, which themselves have been introduced to Yakutia to fulfill a similar niche.
• Tarpan – A population of free-ranging horses in Europe that went extinct in 1909. Much like the aurochs, there have been many attempts to breed tarpan-like horses from domestic 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.[66] 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.[67] Other breeds of supposedly tarpan-like horse include the Konik and Strobel's horse.
• Baiji[52]
• Steller's sea cow[57][52]
• Woolly rhinoceros[57][52]
• Japanese sea lion

• Floreana Island tortoise – In 2008, mitochondrial DNA from the Floreana tortoise species was found in museum specimens. In theory, a breeding program could be established to "resurrect" a pure Floreana species from living hybrids.[68][69]

• Gastric-brooding frog – In 2013, scientists in Australia successfully created a living embryo from non-living preserved genetic material, and hope that by using somatic-cell nuclear transfer methods, they can produce an embryo that can survive to the tadpole stage.[57][70]

Museum specimens of the Xerces blue, an extinct butterfly

• Xerces blue[57]

• Rapa Nui palm[57]