Eco-de-extinction
The strategy of Eco-de-extinction is to use the genomic blueprint of an extinct organism as the guide to producing the ideal surrogate population of organisms to assume the ecological role of that extinct organism.

The product of Eco-de-extinction is not a duplicate of an extinct species, but a new population of individuals that performs an ecological role differentially than their relatives: an ecotype.
Supporting principle: Species adapt phenotypes, such as body shape, behavior, and physiological processes to their environment. Interactions with other organisms also heavily shape a species’ adaptation. Many phenotypes are directly controlled and created by genes. The genome of every species has been shaped through evolution to the environment and coevolution with other species, and is a record of the traits that influence species ecology. This form of de-extinction works very much from the guiding principle of the “central dogma” of genetics, extending the dogma of genotype to phenotyp to the ecosystem level. This gives us the Eco-de-extinction dogma:

genotype_phenotype_ecotype

 

Methods
Quantitative De-extinction
The image below depicts methods of Quantitative De-extinction – the use of breeding strategies and quantitative genetics (the study and manipulation of inherited traits) to generate extinct phenotypes.

Quantitative_Deextinction

 

Artificial Selection

In some instances the phenotype that affects a species’ ecology can be generated through breeding of a related species, such as the Quagga Project depicted. The Quagga Project has been breeding plains zebras to recreate the coloration of the extinct Quagga for 5 generations as of 2014. The extinct quagga had very distinct coloration – no striping on the legs, a dark brown base color, and reduced striping on the flanks. Researchers discovered plains zebras with fewer stripes on their hind legs. Through successive breeding the team has produced what they call “Rau” quaggas, which quantitatively fall within the historic variance of extinct quagga stripe patterns. Continued breeding will work to reproduce the rich brown color.

The result of artificial selection is not the original extinct species, but a new strain of living species that recapitulates the extinct species form. This method is most suited to closely related subspecies.

Why does color matter? Coloration is important in nature from camouflage to controlling body temperature. Many herding species, like zebra, use coloration as a form of social communication and to confuse predators.

Backbreeding

When an extinct species leaves multiple lines of descendants, the actual ancestral genes associated with the extinct species traits can be bred back together. In the case of the Aurochs this is being done currently.

All living cattle breeds were developed originally from the Aurochs. Each breed has been selected to exaggerate traits and new mutations, but each breed contains the genomic backbone of the Aurochs and certain breeds retain particular phenotypes. By crossing these breeds in various ways the extinct phenotype of the Aurochs, notably its large size, dietary capability, and robust wild-survival skills can be concentrated into a new breed that can take on the former natural role of the Aurochs, which once ranged throughout Europe and Asia.

Hybrid Selection

Many species hybridize naturally where their ranges overlap, or hybridize when the opportunity is provided – such as in captivity or when an individual wanders out of native range. First generation hybrids of two species are equal genetic parts of each parent species: 50/50. When hybrids then breed with one or the other parent species they accumulate different proportions of genes, and their chromosomes rearrange to carry the genes of both species. When humans left Africa they came into contact with Neanderthals – and today many people carry traces of Neanderthal DNA from that ancient meeting.

By crossing hybrids in the right manner the genes of one parent species can be accumulated and phenotypes created by that parent species’ genes can dominate.

No projects currently are attempting to use hybrid selection breeding to reconstitute an extinct species traits, but Hybrid galapogos tortoises have been discovered carrying genes of the now extinct Pinta Island tortoise, made famous by the life of “Lonesome George”, who died in 2012. The right breeding could reproduce a population comprised largely of Pinta Island tortoise genes, conferring phenotypes uniquely adapted to Pinta Island.

Engineered Ecotype De-extinction

When no living relatives of a species possess hybrid or descendant genes or malleable phenotypes the traits of an extinct organism can be recreated through engineering.  This is the case for most extinct species.  Luckily, the genes of extinct species can be sequenced from fossil specimens and preserved remains, such as skins and fluid specimens in museum collections. Fragmentary DNA sequences from diverse extinct organisms has been sequenced for over 30 years, and now complete genomes of extinct organisms are being sequenced.

In concept the procedure is simple: Identify genes that create significant traits, engineer those traits into a living related organism, and then reproduce those organisms and restore them to the wild through established means of reintroduction.  The CRISPR-Cas9 genome editing tool is what makes this possible. CRISPRs allow for precise genome editing by targeting specific DNA sequences. The genes of the living species can be removed and then replaced with DNA molecules matching the genetic code of an extinct species.

Simple in principle, but this task will be the greatest undertaking conservation science has ever attempted. Current projects include the Passenger Pigeon and Woolly Mammoth, while other species, such as the Thylacine have been proposed and are likely to begin in the near future.

 

 

Ecotype_deextinction

Reintroducing a thylacine ecotype to Tasmania would restore the role of an apex predator – one coevolved with the native marsupial prey, which are overkilled by introduced placental predators. Apex predators have major effects on ecosystems, with “top down” food web impacts that result in productive biodiversity.

Many remains exist to obtain DNA sequences. The tasmanian devil is the most suitable living species to recreate the thylacine.

Dense flocks of passenger pigeons were a major driver of forest disturbance cycles in eastern North America. Over millenia the woodland ecosystems became disturbance regime communities of species coevolved to use various disturbance habitats. New passenger pigeons would aid in re-establishing disturbance cycles that hundreds of species need to thrive.

This keystone species is the flagship project of Revive & Restore. The passenger pigeon genome has been sequenced and over 80% of the code has been pieced together. In the coming months more gaps will be filled in and genome editing experiments are targeted to start in the next 3 years.

The mammoth was the major ecosystem engineer of northern climes, once home to immensely abundant populations of grassland species. Mammoths were the largest distributors of nutrient cycling and the only grazer capable of clearing trees for expanding grassland habitat.

The full mammoth genome is almost finished – the subject of an international research effort. Mammoth mutations are already being engineered into living elephant cells at Dr. George Church’s lab at Harvard through a joint project with Revive & Restore. Dr. Church is planning to recreate mammoths in less than a decade.