Genetics of the passenger pigeon: The now-extinct passenger pigeon used to be one of the most numerous vertebrates on Earth. Murray et al. examined the genomes of four passenger pigeon samples from different locales within its range. They describe the interplay between passenger pigeon population size, genome structure and recombination, and natural selection. They conclude that a reduction in genetic diversity provided few avenues for the bird to respond to human pressures, which ultimately drove it to extinction. Science , this issue p. 951

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.

Conservation translocations (reintroductions, reinforcements, ecological replacements, and assisted colonization) have played a vital and necessary role in conserving endangered species and ecosystems. Yet concerns over potential unintended ecological consequences frequently hinder the progress of translocation activities. We reviewed the history of U.S. translocations to ask: how often were intended benefits the result versus harmful unintended consequences? We found that translocations played a key role in recovery for 30% (14 of 47) of U.S. delisted taxa. Translocations have been performed, are planned, or are part of continuing recovery actions for 70% (1,112 of 1,580) of listed threatened and endangered taxa. Of the 1,014 total taxa we found with recorded conservation translocations spanning 125 years, we found only one restricted instance that caused a loss of biodiversity. All other reports of negative consequences were caused by translocations performed for economic and cultural interests in the absence of conservation‐based governance. Examples included fish stocking for sport and biological control programs for agricultural pests. We included biological control programs in this analysis because they can be and often are used as conservation tools, to directly benefit ecosystems. In addition, they are often raised as examples of harmful unintended results during the conservation planning process. However, only 1.4% (42) of 3,014 biological control agents released globally have caused ecosystem‐level deleterious impacts. All of these were initially released before the 1980s and conservation‐based practice and governance in recent decades have reduced off‐target impacts from biological control practice. Two themes emerged from our review: (a) conservation translocations routinely yielded their intended benefits without producing unintended harm, and (b) when ecological damage did occur, it was in the absence of conservation practice and regulation. This evidence shows that well‐planned translocation efforts produce ecosystem benefits, which should be weighed against the costs of inaction when deliberating conservation strategies.

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These ‘soft tissues’ have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil ‘soft tissues’ differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species.

Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group’s evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.