Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but there are few guidelines for integrating GRBs into established breeding programs. Here we present basic guidelines, focusing on strategies for the collection, maintenance, and use of semen GRBs for protecting genetic diversity. These guidelines should be applied in the context of the specific purposes and roles of a breeding program's GRB, which will differ among species depending on vulnerability to loss and the status of rescue and conservation efforts. We recommend establishing up to three types of collections: (1) a National Reserve to preserve a species' genetic diversity, to be used only as a last resort; (2) a Savings Account to be used periodically to invigorate a genetically depauperate population; and (3) a Checking Account to be used as a regular part of the breeding program. We present methods for identifying donors to maximize genetic diversity in a GRB, as well as strategies for maintaining and optimally using GRBs.

Insurance populations can provide a short-term safeguard for at-risk species. The goal for all insurance populations should be to maintain a high welfare, genetically diverse, self-sustaining population that is available for eventual reintroduction of animals back into the wild when it is safe to do so. However, many insurance populations in zoos are not meeting sustainability goals, and there is a need for larger conservation centers and sanctuaries, a greater focus on threatened species, and metapopulation management between independently managed populations. Within North America, privately-owned ranches frequently maintain large populations of threatened ungulates that are presently managed independently from AZA-accredited zoos. Using a large set of single nucleotide polymorphisms, we generated empirical kinship and genetic distance estimates for AZA and private ranch populations of southern sable antelope (Hippotragus niger niger) and critically endangered addra gazelle (Nanger dama ruficollis). We used stochastic population models to project population mean kinship (mk) and founder genome equivalents (FGE) over time with and without genetic metapopulation management, using empirical kinships and genetic distances to guide transfers. Mean kinship-guided transfers were consistently beneficial for all study populations, for both species. Genetic distance-guided transfers, however, resulted in modest population mk increases for AZA populations, but predicted remarkable decreases in population mk for ranch populations. Although predicted benefits varied depending on management approach, our results show that a metapopulation management plan, whether mutually beneficial or altruistic, best supports species conservation by mitigating the loss of genetic diversity, minimizing the possibility of inbreeding, and yielding genetically diverse animals.

Maintaining a living plant collection is the most common method of ex situ conservation for plant species that cannot be seed banked (i.e., exceptional species). Viability of living collections, and their value for future conservation efforts, can be limited without coordinated efforts to track and manage individuals across institutions. Using a pedigree-focused approach, the zoological community has established an inter-institutional infrastructure to support long-term viability of captive animal populations. We assessed the ability of this coordinated metacollection infrastructure to support the conservation of 4 plant species curated in living collections at multiple botanic gardens around the world. Limitations in current practices include the inability to compile, share, and analyze plant collections data at the individual level, as well as difficulty in tracking original provenance of ex situ material. The coordinated metacollection framework used by zoos can be adopted by the botanical community to improve conservation outcomes by minimizing the loss of genetic diversity in collections. We suggest actions to improve ex situ conservation of exceptional plant species, including developing a central database to aggregate data and track unique individuals of priority threatened species among institutions and adapting a pedigree-based population management tool that incorporates life-history aspects unique to plants. If approached collaboratively across regional, national, and global scales, these actions could transform ex situ conservation of threatened plant species.

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in natural outbreeders. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. Crossing between populations also enhances the ability to evolve. Outbreeding depression result primarily from populations belonging to different taxa, having fixed chromosome differences, being genetically adapted to different environments, having a long history of isolation, or to combinations of these, and can be avoided by screening out population combinations with these characteristics.

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of wild animal and plant populations decreases and fragmentation increases, inbreeding reduces fitness and loss of genetic diversity reduces their ability to adapt to changes in the environment. Many small isolated populations are going extinct unnecessarily. In many cases, such populations can be genetically rescued by gene flow from another population within the species, but this is very rarely done. This book provides a practical guide to the genetic management of fragmented animal and plant populations.

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift), and gene flow. Large outbreeding sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

When the decision is made to initiate gene flow into an isolated population, managers must decide when to start, from where to take the individuals or gametes, how many, which individuals, how often, when to cease, etc. Even without detailed genetic data, sound management strategies for augmenting gene flow can be developed by considering conservation genetics theory or using computer simulations. Moving some individuals into isolated inbred population fragments is better than moving none. With more detailed genetic information, more precise genetic management of fragmented populations can be achieved, leading to improved genetic outcomes. Gene flow management will be most effective if done using mean kinship (estimated from modeling, genetic markers, or pedigrees), and moving individuals from the fragment with the lowest mean kinships into the target fragment(s). Further improvements can be made using individual kinships to choose the best individuals to move. Populations should then be monitored to confirm that movement of individuals has enhanced genetic diversity and fitness.

Most species now have fragmented distributions, often with adverse genetic consequences. The genetic impacts of population fragmentation depend critically upon gene flow among fragments and their effective sizes. Fragmentation with cessation of gene flow is highly harmful in the long term, leading to greater inbreeding, increased loss of genetic diversity, decreased likelihood of evolutionary adaptation and elevated extinction risk, when compared to a single population of the same total size. The consequences of fragmentation with limited gene flow typically lie between those for a large population with random mating and isolated population fragments with no gene flow.

The first step in conservation management is to delineate groups for separate versus combined management. However, there are many problems with species delineation, including diverse species definitions, lack of standardized protocols, and poor repeatability of delineations. Definitions that are too broad will lead to outbreeding depression if populations are crossed, while those that split excessively may preclude genetic rescue of small inbred populations with low genetic diversity. To minimize these problems, we recommend the use of species concepts based upon reproductive isolation (such as the Biological Species Concept) and advise against the use of Phylogenetic and General Lineage Species Concepts. We provide guidelines as to when taxonomy requires revision and outline protocols for robust species delineations.

Even without detailed genetic data, sound genetic management strategies for augmenting gene flow can be instituted by considering population genetics theory, and/or computer simulations. When detailed data are lacking, moving (translocating) some individuals into isolated inbred population fragments is better than moving none, as long as the risk of outbreeding depression is low. With more detailed genetic information, more precise genetic management of fragmented populations can be achieved. Using mean kinship within and between populations (estimated from modeling, pedigrees, genetic markers or genomes), and moving individuals among fragments with the lowest between fragment mean kinships provides the best approach to gene flow management. Populations should then be monitored to confirm that movement of individuals has resulted in the desired levels of gene flow, genetic diversity has been enhanced, and that the status of the population is improving.

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

Inbreeding depression, accumulation and loss of deleterious mutations, loss of genetic variation in small populations, genetic adaptation to captivity and its effect on reintroduction success, and outbreeding depression are reviewed. The impact of genetic factors in endangerment and extinction has been underestimated in some recent publications. Inbreeding depression in wildlife and in the field has been clearly established, while its impact has been greatly underestimated. The size of populations where genetic factors become important is higher than previously recognized, as Ne/N ratios average 0.11. Purging effects have been overestimated as a mechanism for eliminating deleterious alleles in small populations. The impact of loss of genetic variation in increasing the susceptibility of populations to environmental stochasticity and catastrophes has generally been ignored. Consequently, extinctions are often attributed to "nongenetic" factors when these may have interacted with genetic factors to cause extinction.

The cheetah's distribution has been severely reduced in the last century, with habitat loss and fragmentation among the principal drivers of decline. All remaining populations are near or below recommended minimum thresholds for extinction risk. Our review suggests that the principal habitat factors are (1) access to sufficient prey, (2) interspecific impacts associated with other carnivores, and (3) the level of human tolerance. The cheetah's biology provides a level of resilience that allows them to disperse great distances and exist in a wide variety of marginal or even extreme habitats. We suggest that additional conservation efforts, designed to increase connectivity and reduce the impacts of habitat fragmentation, are needed outside of traditional focal areas for cheetah. In particular, connectivity conservation efforts should focus on reducing predator–human conflicts and maintaining adequate prey density in marginal habitats with low agricultural cultivation risk, where the primary land-use is nomadic livestock herding.

Thousands of small populations are at increased risk of extinction because genetics and evolutionary biology are not well‐integrated into conservation planning–a major lost opportunity for effective actions. We propose that if the risk of outbreeding depression is low, the default should be to evaluate restoration of gene flow to small inbred populations of diploid outbreeding organisms that were isolated by human activities within the last 500 years, rather than inaction. We outline the elements of a scientific‐based genetic management policy for fragmented populations of plants and animals, and discuss the reasons why the current default policy is, inappropriately, inaction.

AbstractHaving identified small geographically and genetically isolated populations, we need to determine whether they are suffering genetic erosion, and if so, whether there are any other populations to which they could be crossed. We should next ask whether crossing is expected to be harmful or beneficial, and if beneficial, whether the benefits would be large enough to justify a genetic rescue attempt. Here, we address these questions based on the principles established in the preceding chapters.

Abstract We recommend augmentation of gene flow for isolated population fragments that are suffering inbreeding and low genetic diversity, provided that proposed population crosses have low risks of outbreeding depression, and the predicted benefits justify the financial costs.