De-extinction

Further information: Breeding back

The Pyrenean ibex, or bucardo, is the first animal to have survived de-extinction past birth.

De-extinction, or resurrection biology, or species revivalism is the process of creating an organism, which is either a member of, or resembles an extinct species, or breeding population of such organisms. Cloning is the most widely proposed method, although selective breeding has also been proposed. Similar techniques have been applied to endangered species.

There is significant controversy over de-extinction, and critics assert that efforts would be better spent conserving existing species, and that the habitat necessary for formerly extinct species to survive is too limited to warrant de-extinction.

Methods

Cloning

Cloning is one method discussed as an option for bringing extinct species back. Proponents include author Stewart Brand, and proposed species include the passenger pigeon and the woolly mammoth. De-extinction efforts are now underway to revive the passenger pigeon by extracting DNA fragments and taking skin samples from preserved specimens and, later, using band-tailed pigeons or rock pigeons as surrogate parents.

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.

A team of Russian and South Korean scientists are, as of April 2013, in the planning stages of cloning a woolly mammoth using an Asian elephant as a surrogate mother. Large amounts of well-preserved mammoth tissue have been found in Siberia. If the process can be completed, there are plans to introduce the mammoths to Pleistocene Park, a wildlife reserve in Siberia. (Evolutionary biologist Beth Shapiro points out that "cloning" is a specific technique which cannot be accomplished without a living cell, none of which are available for mammoths, but suggests genome editing might be feasible.)

Although de-extinction efforts have not yet succeeded in producing viable offspring of a previously extinct species, the same process has been applied successfully to endangered species. The banteng is the second endangered species to be successfully cloned, and the first to survive for more than a week (the first was a gaur that died two days after being born). Scientists at Advanced Cell Technology in Worcester, Massachusetts, United States extracted DNA from banteng cells kept in the San Diego Zoo's "Frozen Zoo" facility, and transferred it into eggs from domestic cattle, a process called somatic cell nuclear transfer. Thirty hybrid embryos were created and sent to Trans Ova Genetics, which implanted the fertilized eggs in domestic cattle. Two were carried to term and delivered by Caesarian section. The first hybrid was born on April 1, 2003, and the second two days later. The second was euthanized, but the first survived and, as of September 2006, remained in good health at the San Diego Zoo.

Scientists from the University of Newcastle and the University of New South Wales reported in May 2013 the successful cloning of the extinct frog Rheobatrachus silus using the process of somatic cell nuclear transfer. The embryos developed for several days but died. In an important development the scientists from Newcastle reported associated technologies that provide a "proof of concept" for the proposal that frozen zoos (also referred to as genome banks and seed banks) are an effective mechanism to provide an insurance against species extinction and the loss of population genetic diversity. They connected the circle between de-extinction and the prevention of extinction for threatened animal species. The important advances were the capacity to successfully recover live frozen embryonic cells from animals that produce large yolky eggs (anamniotes such as fishes and amphibians) When this development is combined with somatic cell nuclear transfer (SCNT) it enables the genome to be recovered. The scientists point out that many embryonic cells can be frozen and when combined with frozen sperm storage enables the genetic diversity of populations to be stored. With groups of vertebrates such as the amphibians facing an extinction crisis they propose this as an effective means to prevent extinction while the causes of declines can be identified and remedied. The technical difference between frozen tissue samples commonly used for genetic studies (e.g. phylogenetic reconstruction) and those in a frozen zoo is the use of cryoprotectants and special freezing rates at the time of freezing and thawing.

Selective breeding

The aurochs, which became extinct in 1627, could possibly be brought back by taking DNA samples from bone and teeth fragments in museums in order to obtain genetic material to recreate its DNA. Researchers would then compare the DNA to that of modern European cattle to determine which breeds still carry the creature's genes, and then undertake a selective breeding program to reverse the evolutionary process. The intention would be that with every passing generation, the cattle would more closely resemble the ancient aurochs.

The quagga, a subspecies of zebra which has been extinct since the 1880s, has been revived using selective breeding of zebras. Since the new animal is not genetically identical to the extinct subspecies, the new animal is called the Rau quagga.

Opposition

Opponents of de-extinction have claimed that efforts, and resources, to resurrect extinct species could have been better used trying to conserve endangered species that might themselves become extinct.

It has also been noted that a resurrected species, while being genetically the same as previously living specimens, will not have the same behaviour as its predecessors. The first animal to be brought back will be raised by parents of a different species (the fetus's host), not the one that died out and thus have differing mothering techniques and other behaviors.

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, for example the black-footed ferret or the northern white rhinoceros. It noted, however, that such research "should be conducted under the mantle of preserving modern biodiversity rather than conjuring extinct species from the grave."

Other scholars have published ethical concerns regarding de-extinction. In Conservation Biology, Robert Sandler argues that introducing extinct species to environments may produce harm to modern species, as invasive species. Issues regarding scientific hubris, human and animal health, and the ecology of sensitive environments have been raised by the scientific community. Further research must be performed regarding de-extinction to investigate advantages and disadvantages to the technology. New technological practices must be examined to prevent environmental hazards.

Potential candidates for de-extinction

Birds

• Passenger pigeon – this species numbered in the billions before being wiped out due to commercial hunting and habitat loss. Using DNA found in museum specimens and skins, the non-profit organization Revive and Restore aims to recreate the passenger pigeon using its closest living relative, the band-tailed pigeon.
• 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 make the moa a candidate for resurrection. New Zealand politician Trevor Mallard has suggested bringing back a medium-sized species.
• 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.
• Dodo – this large, flightless ground bird endemic to Mauritius became extinct in the 1640s due to exploitation by humans and due to introduced species such as rats and pigs, which ate their eggs. 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
• Huia
• Oʻo
• Elephant bird

Mammals

• Woolly mammoth – 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 is cloning, which would involve removal of the DNA-containing nucleus of the egg cell of a female elephant, and replacement with a nucleus from woolly mammoth tissue. The cell would then be stimulated into dividing, and inserted back into a female elephant. The resulting calf would have the genes of the woolly mammoth, although its fetal environment would be different. To date, 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.

The second method involves artificially inseminating an elephant egg cell with sperm cells from a frozen woolly mammoth carcass. The resulting offspring would be an elephant–mammoth hybrid, and the process would have to be repeated so more hybrids could be used in breeding. After several generations of cross-breeding these hybrids, an almost pure woolly mammoth would be produced. The fact that sperm cells of modern mammals are potent for 15 years at most after deep-freezing is a hindrance to this method. In one case, an Asian elephant and an African elephant produced a live calf named Motty, but it died of defects at less than two weeks old.

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. In 2011, Japanese scientists announced plans to clone mammoths within six years. As the woolly mammoth genome has been mapped, a complete strand of DNA may be synthesised in the future. Mammoth expert Adrian Lister questions the ethics of such recreation attempts. In addition to the technical problems, he notes that there is not much habitat left that would be suitable for woolly mammoths. Because the species was gregarious, creating a few specimens would not be ideal. He also notes that the time and resources required would be enormous, and that the scientific benefits would be unclear; these resources should instead be used to preserve extant elephant species which are endangered. However, it was reported in March 2014 that blood recovered from a frozen mammoth carcass in 2013 now provides a "High chance" of cloning the woolly mammoth, despite previous hindrances.

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, and 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.

A revived woolly mammoth or mammoth-elephant hybrid may find suitable habitat in the tundra and taiga forest ecozones, and may also find refuge in Pleistocene Park, a Pleistocene rewilding experiment by Russian scientist Sergey Zimov to recreate the mammoth steppe, the former habitat of the woolly mammoth. While mammoths are not required for the recreation of the steppe, they would be highly effective in doing so by quickly clearing brush and forest and allowing grasses to colonize the area, a capability that modern arctic megafauna do not have.

• Pyrenean ibex – This was one of four original subspecies of Spanish ibex that roamed on the Iberian peninsula. However, while it was abundant during Medieval times, over hunting in the 19th and 20th century lead 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 still seen as a triumph and has been considered to have been the first de-extinction. However, 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 the fact 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.
• Aurochs – This species 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. This species is heavily featured in European cave paintings, such as Lascaux and Chauvet cave in France, and was still widespread during the Roman era, in which they were used as fighting animals for entertainment, and were noted by Julius Caesar for their strength and prowess. Following the fall of the Roman empire, however, overhunting of the aurochs by nobility and royalty caused its population to dwindle to a single population in the Jaktorów forest in Poland, where the last wild aurochs, a female, died of natural causes in 1627. However, because the aurochs is ancestral to the majority of modern cattle breeds and has close relatives in primitive cattle breeds, it is possible for the aurochs (or a superficial ecological replacement) to be brought back through artificial selection. The first attempt at this was by Heinz and Lutz Heck to recreate the aurochs 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. 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. This organization is partnered with the organization Rewilding Europe to help restore balance to European nature. 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. 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.
• Quagga - This subspecies of the plains zebra was distinct in that it while it was striped on its face and upper torso, its rear abdomen was a solid brown. It was native to South Africa, but was wiped out in the wild due to over hunting for sport, and the last individual died in 1883 in the Amsterdam zoo. 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 quagga through the artificial selection of plains zebras, and 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. Having started in 1984, the project now stands at 110 animals in 10 locations, and individuals have begun to show a reduction in stripes and a browning of the fur, owing to the success of the project.
• The Thylacine is commonly known as the Tasmanian tiger (because of its striped lower back) or the Tasmanian wolf. Native to continental Australia, 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, but it survived on the island of Tasmania along with several other endemic species, including the Tasmanian devil. Intensive hunting encouraged by bounties is generally blamed for its extinction, but other contributing factors may have been disease, the introduction of dogs, and human encroachment into its habitat. Despite its official classification as extinct, sightings are still reported, though none has been conclusively proven. The last know thylacine died at Beaumaris Zoo in Hobart, Tasmania on 7 September 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. National Threatened Species Day has been held annually since 1996 on 7 September in Australia, to commemorate the death of the last officially recorded thylacine. Although there had been a conservation movement pressing for the thylacine's protection since 1901, driven in part by the increasing difficulty in obtaining specimens for overseas collections, political difficulties prevented any form of protection coming into force until 1936. Official protection of the species by the Tasmanian government was introduced on 10 July 1936, 59 days before the last known specimen died in captivity. The thylacine held the status of endangered species until the 1980s. International standards at the time stated that an animal could not be declared extinct until 50 years had passed without a confirmed record. Since no definitive proof of the thylacine's existence in the wild had been obtained for more than 50 years, it met that official criterion and was declared extinct by the International Union for Conservation of Nature in 1982 and by the Tasmanian government in 1986. The species was removed from Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in 2013.

The Australian Museum in Sydney began a cloning project in 1999. The goal was to use genetic material from specimens taken and preserved in the early 20th century to clone new individuals and restore the species from extinction. Several molecular biologists have dismissed the project as a public relations stunt and its chief proponent, Mike Archer, received a 2002 nomination for the Australian Skeptics Bent Spoon Award for "the perpetrator of the most preposterous piece of paranormal or pseudo-scientific piffle." In late 2002, the researchers had some success as they were able to extract replicable DNA from the specimens. On 15 February 2005, the museum announced that it was stopping the project after tests showed the DNA retrieved from the specimens had been too badly degraded to be usable. In May 2005, Archer, the University of New South Wales Dean of Science at the time, former director of the Australian Museum and evolutionary biologist, announced that the project was being restarted by a group of interested universities and a research institute. The International Thylacine Specimen Database was completed in April 2005, and is the culmination of a four-year research project to catalog and digitally photograph, if possible, all known surviving thylacine specimen material held within museum, university and private collections. The master records are held by the Zoological Society of London. In 2008, researchers Andrew J. Pask and Marilyn B. Renfree from the University of Melbourne and Richard R. Behringer from the University of Texas at Austin reported that they managed to restore functionality of a gene Col2A1 enhancer obtained from 100-year-old ethanol-fixed thylacine tissues from museum collections. The genetic material was found working in transgenic mice. The research enhanced hopes of eventually restoring the population of thylacines. That same year, another group of researchers successfully sequenced the complete thylacine mitochondrial genome from two museum specimens. Their success suggests that it may be feasible to sequence the complete thylacine nuclear genome from museum specimens. Their results were published in the journal Genome Research in 2009. Mike Archer spoke about the possibilities of resurrecting the thylacine and the gastric-brooding frog at TED2013. Stewart Brand spoke at TED2013 about the ethics and possibilities of de-extinction, and made reference to thylacine in his talk.

• Cave lion - The discovery of two preserved cubs in the Sakha Republic ignited a project to clone the animal.

See also

• Holocene extinction
• Endling

Further reading

• M. R., O'Connor (2015). Resurrection Science: Conservation, De-Extinction and the Precarious Future of Wild Things. New York: St. Martin's Press. ISBN 9781137279293. 
• Shapiro, Beth (2015). How to Clone a Mammoth: The Science of De-Extinction. Princeton, NJ: Princeton University Press. ISBN 9780691157054. 

External links

• TEDx DeExtinction March 15, 2013 conference sponsored by Revive and Restore project of the Long Now Foundation, supported by TEDx and hosted by the National Geographic Society, that helped popularize the public understanding of the science of de-extinction. Video proceedings, meeting report, and links to press coverage freely available.
• De-Extinction: Bringing Extinct Species Back to Life April 2013 article by Carl Zimmer for National Geographic magazine reporting on 2013 conference.