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Ben Jacob Novak. Genes (Basel).


De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In 2016, a special committee of the International Union for the Conservation of Nature (IUCN) published a set of guidelines for de-extinction practice, establishing the first detailed description of de-extinction; yet incoherencies in published literature persist. There are even several problems with the IUCN definition. Here I present a comprehensive definition of de-extinction practice and rationale that expounds and reconciles the biological and ecological inconsistencies in the IUCN definition. This new definition brings together the practices of reintroduction and ecological replacement with de-extinction efforts that employ breeding strategies to recover unique extinct phenotypes into a single "de-extinction" discipline. An accurate understanding of de-extinction and biotechnology segregates the restoration of certain species into a new classification of endangerment, removing them from the purview of de-extinction and into the arena of species' recovery. I term these species as "evolutionarily torpid species"; a term to apply to species falsely considered extinct, which in fact persist in the form of cryopreserved tissues and cultured cells. For the first time in published literature, all currently active de-extinction breeding programs are reviewed and their progress presented. Lastly, I review and scrutinize various topics pertaining to de-extinction in light of the growing body of peer-reviewed literature published since de-extinction breeding programs gained public attention in 2013.

Keywords: de-extinction; evolutionarily torpid species; heath hen; passenger pigeon; precise hybridization; proxy; restore; revive & woolly mammoth.

Conflict of interest statement

The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript and in the decision to publish the results.


Figure 1
Figure 1
Graphic representation of ecological and biological lineages of species through time to compare and contrast examples of assisted recovery and de-extinction. The examples display the parallel nature of recovery and de-extinction techniques with the restoration of ecological function ensuing from the return or introduction of species to the wild (in situ). As can be seen, the genetic lineage of recovered species never breaks but persists, while in de-extinction efforts the original historic species, subspecies, or population is extinct or altered, requiring a new form to replace it. For the aurochs, it is clear that the lineage is unbroken but has been altered through historic and modern day breeding. For the passenger pigeon, some of the genetics from the historic lineage are recovered in the hybrid proxy lineage. The black-footed ferret is an excellent example of an extant species through which biotechnology has been used to assist recovery; cryopreserved semen has been used to retrieve historic genetics and maintain diversity in the population [29]. Revive & Restore has initiated work to test cloning in black-footed ferrets from cryopreserved cells at the SDZGFZ, which may recover the genetics of two deceased individuals that would represent new founders to the population [30]. Progress for each program is predicted beyond the present to show the intended goals of nascent projects. In the case of northern white rhinoceros recovery, the projected timeline shows a break in the ex situ lineage representing the eventual death of the last two surviving adults, which may or may not occur before a new generation of offspring are produced via stem cell embryogenesis or cloning.
Figure 2
Figure 2
The de-extinction process via precise hybridization. The sequential stages begin with in silico and end in situ, shown on the outside circle. The inner circle shows the compartmentalized and overlapping supporting research for the de-extinction process, with arrows showing exchange of resources (dark purple are physical resources, light purple are knowledge resources). Passenger pigeon de-extinction is a model example of this research process, the genomes of the template species were sequenced from a wild individual (in situ), a captive individual (ex situ) and embryonic fibroblast cultures (in vitro), [58]. The sequencing of those genomes has been key to understanding the species’ role as an ecosystem engineer [100], (in silico to in situ insight pathway). Currently, program collaborators are using newly developed bioinformatic pathways [111] to identify candidate passenger pigeon alleles for de-extinction purposes using a comparative genomics process that compares species pairs based upon shared/derived phenotypes (in situ to in silico insight pathway). The species’ ecology has been clarified further through ex situ observations of band-tailed pigeon digestion and in situ experiments to understand seed dispersal and predation [112]. The program has studied the animal husbandry of the template species [113] and used tissues from one of the Bronx Zoo individuals of that study to improve the Murray et al. genome sequence to a chromosomal level assembly (unpublished). Recently the program has begun genetic engineering research using domestic pigeons to facilitate functional genomics research in vivo [114]. Domestic pigeon primordial germ-cell cultures have been preliminarily tested for advancing the eventual in vitro to in vivo progression to create hybrid proxies; the pilot study did not successfully culture cells long term but produced data for staging embryonic development for optimal isolation of germ cells [115].

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