Current and Future Genetic Technologies for Wildlife Management

Symposium
ROOM: CC, Room 25A
SESSION NUMBER: 27
 
Rapid advances in analytical technologies have allowed for the economic and practical gathering of genetic information of individuals and wildlife populations at a landscape and temporal scale previously not possible. These technological advances are currently being implemented into various management efforts for disease and invasive species detection and control. However, useful the current approaches are, they are based on basic methodologies identified 30-50 years ago. Newer advances in our understanding of genes and gene expression are opening up the possibility of moving beyond characterizing genetic aspects of wildlife populations. Specifically, gene silencing and gene editing approaches, among others, are already being developed and reduced to practice in the fields of medicine, chemical production, chemical hazard remediation, and agriculture. The era of synthetic biology is upon us. These technologies hold the promise of designing species-specific management tools for pest control and conservation. But there is uncertainty of risk and rewards of the promise and function of these technologies in the world outside of a laboratory setting, and how these technologies compare to existing methods for management. This symposium will examine what genetic methods are being used now, and what synthetic biology methods are likely to be brought to the wildlife community in the future. Discussions will also focus on the risks and rewards of such technologies, and most importantly, how these technologies will fit into a social framework of concerns and acceptance.

12:50PM The Need and Promise for New Technologies for Human-Wildlife Conflict
  Larry Clark
Yesterday’s discoveries are todays technologies and management tools. Today’s discoveries are tomorrow’s management tools. However, getting from idea, to product, to use, is an endeavor fraught with challenges. This process is exemplified by the field of genetics. In this symposium we aim to bring to a broader wildlife management audience an appreciation of how yesterday’s discoveries along with technological advances are being used for today’s wildlife management needs and challenges that include understanding population structure and movement, disease ecology, and conservation applications. Our speakers will also touch upon how our understanding of the mechanisms of the genetic central dogma (transcription and translation) has advanced and what it means for wildlife management, conservation, and invasive species management. But these advances and proposed applications also bring us into the arena of what is called synthetic biology (gene editing) which place us into areas of regulation and policy where the clarity on how to use these technologies lags behind the technologies themselves. Perhaps most importantly, while these technical and policy issues are being harmonized, the public is being introduced to bits and pieces of the debate. Our ultimate challenge will not be the technical, but will be engagement of the public during this process. All the promise and reward will never come to fruition unless there is an integration of the science with public perception, concern, and participation throughout the development process. Every wildlife biologist is a member of some community. It is our goal through this symposium to provide wildlife biologists with some of the information they may need now and into the future on the risk, rewards, concerns, and solutions on how old and new technologies have come about, how they are used, and what options may be available as we move forward.
1:10PM High-Throughput Sequencing and Wildlife Surveillance: Invasive Species, Conservation, and Disease
  Matt W. Hopken; Zaid Abdo; Antointte J. Piaggio
High-throughput sequencing has revolutionized the way we discover and identify biodiversity. From soil microbes to elusive vertebrates, we now have the ability to detect an extremely broad range of taxonomic groups with high sensitivity and precision, some of which were previously unknown to science. The fields of metagenomics and metabarcoding have now moved beyond basic science and are actively part of wildlife management. For example, these approaches have been used to detect the presence of invasive and endangered species without direct observation, species involved in human-wildlife conflicts, predators of sensitive prey species, as well as pathogens and their hosts from environmental samples, fecal samples, and hematophagous invertebrate blood meals. During this presentation, I will explain the technical aspects of metagenomics and metabarcoding, highlight examples from the literature and our labs, and discuss the pros and cons of each approach. I will then discuss additional sequencing technologies that are currently under beta-testing in wildlife genetics and have the potential to move the field to the next level.
1:30PM Today: Landscape Uses for Genomic Information (Defining Management Units/Source-Sink Populations
  Timothy J. Smyser; Antoinette J. Piaggio
The description of population genetic structure has been a foundational question of wildlife ecology since the extension of molecular tools to the field. With the wide-spread use of microsatellites, genetic clustering and assignment testing became standard analyses of landscape genetics for the delineation of populations and identification of genetic migrants. As low density single nucleotide polymorphism (SNP) genotyping, with tens or hundreds of loci, began to appear among wildlife datasets, this new marker type could be directly substituted into many of the well-established population genetic analyses developed for microsatellites. However, the emergence of high density SNP datasets, with tens of thousands of markers, has provided unprecedented genetic resolution while also creating data management and computational challenges and requiring the development of new analyses approaches. Using data generated with a high density SNP array, we illustrate a population genomic analysis of feral swine (Sus scrofa; also known as invasive wild pigs) for Missouri, USA. We implemented a geometric approach using principal component analysis and related methods to graphically illustrate differences among populations. Additionally, we used a genetic model based approach implemented in ADMIXTURE to describe genetic structure in an unsupervised framework. Despite having phenomenal genetic resolution, we encountered conditions in which multiple management units fell within a single genetic cluster. In order to provide genetic guidance under such challenging conditions, we develop, here, an approach that integrates the concepts of cluster analysis, permutations, and assign testing to identify patterns of connectivity among management units that associate as a single genetic cluster. In sum, high resolution SNP datasets offer tremendous advantages over traditional microsatellite datasets with statistical analyses now emerging that allow biologists to truly harness the unprecedented genetic resolution to address management questions.
1:50PM 21st Century Technologies for Highly Endangered Species: Cloning, Gene Editing, and Epigenetic Manipulation for Conservation
  Samantha Wisely
Life science technology flows from one discipline to another in a predictable pattern. Technology is typically developed by biomedical scientists, is adopted by veterinary medicine and eventually trickles down to conservation practice. As a result, the toolbox of conservation has gradually expanded to include a repertoire of technologies including artificial insemination, cryopreservation, and whole genome characterization. These technologies have allowed conservation practitioners to enhance the genetic health of populations and define distinct population segments for conservation. A new wave of technologies in reproductive science and molecular manipulations is again poised to advance the management of threatened and endangered species. Cloning, which is regularly used in veterinary science to perpetuate the genomes of individual animals across generations, is being considered as a way to increase gene diversity in captively managed endangered populations. Gene editing offers the potential to erase the impact of mutational meltdown in inbred species, or provides species with alleles that permit populations to keep pace with global change. Epigenetic manipulation may help species that are threatened with emerging diseases defend themselves against the threat more efficiently. While none of these technologies has been applied to T&E species, many of them have been proposed by conservation scientists and are under consideration by regulatory agencies. It is imperative that conservation practitioners and wildlife managers understand these technologies, their risks and rewards so that they can participate in the ongoing discussions of their utility and bioethics.
2:10PM Tomorrow: Gene Silencing and the Next Generation of Species Specific Pesticides
  Katherine Horak
Invasive species cause devastating damage to both agriculture and ecosystems worldwide. Feral swine cause significant loss of crop yield from both killing plants and ruining landscape. Invasive rodents are commonly found on islands, historically free of these animals, and have negative impacts on both native plant and animal species. Rodents are exceptionally well adapted to their environments and therefore, quite challenging to control. Current control strategies of pest species often include large scale applications of toxicants, which may have potential adverse effects on non-target wildlife. Therefore, the development of new species specific toxicants will be a valuable advancement in the effort to control pest species. To that end, we are investigating the use of RNA interference, RNAi, as a novel way to control pest species. RNAi is a new technology that has shown much promise as both a therapeutic for human diseases and in the efforts to control insects and plant diseases. In essence, RNAi is a gene-silencing technology in which small, specifically designed sequences of RNA are introduced into cells and induce the degradation of sequences of RNA encoding a target gene of interest. This degradation of RNA means that the protein for which the RNA was coding is no longer synthesized. By inhibiting protein synthesis, RNAi enables researchers to selectively alter cell function in both normal and disease states. By screening the target animal genome, selecting genes of interest, and comparing the sequences of these genes to non-target species, we are able to choose genes that are present in the pest species and not in the non-target species. Therefore, if non-target species consume the RNAi they will not be effected. The use of RNAi as a method to control pest species shows promise because of its species specificity and low non-target impact.
2:30PM Refreshment Break
3:20PM Development, Decision-Making and Implementation of Gene-Edited Mice for Eradication of Invasive Rodents on Islands
  J Royden Saah; Megan Serr; Antoinette J. Piaggio; John Eisemann; Heath Packard
Invasive rodents cause extinctions on islands contributing to the global loss of biodiversity. To protect the native species threatened by these mammals, eradication efforts are undertaken, which almost exclusively use anticoagulant rodenticides. The Genetic Biocontrol of Invasive Rodents (GBIRd) program is an international effort to explore and responsibly develop gene-editing technologies to safely replace rodenticide use on islands. Multiple approaches are being examined for ability/appropriateness to affect invasive rodent populations by biasing the sex ratio to allow eradication via attrition. Creating an all-male or all female population could hypothetically be done by linking sex-determining elements to genetic mechanisms including CRISPR-Cas9 or t-complex meiotic drive found in Mus musculus. A key consideration of GBIRd is the safety of the proposed technology both in terms of containment and possible negative and beneficial effects to the environment. Multiple biosafety mechanisms are being evaluated to limit the functionality of any genome-edited mice to the desired invasive population. Throughout this development effort, early and active engagement is occurring with regulatory authorities in countries where this technology is being considered. GBIRd’s primary tenet of transparency allows significant opportunity for engagement with conservation stakeholders, affected communities, regulatory agencies, and other publics to facilitate a mutual understanding of the risks and benefits of this technology. Our goal is transparent investigation of the efficacy, safety and practicality of this technology as a new way to conserve our diminishing biodiversity.
3:40PM Environmental and Regulatory Considerations for Genetic-based Wildlife Management Tools
  John D. Eisemann; Emily W. Ruell
A growing wave of new genetics-based products for wildlife management is on the horizon. Vaccines incorporating recombinant RNA (rRNA) have been used to control raccoon rabies for decades, and rRNA vaccines to combat plague in prairie dogs have recently been introduced into the wildlife manager’s tool box. New technologies being developed and tested directly modify a target organism’s genome through the delivery of interfering RNA (RNAi). These products are applied by injection, direct ingestion via treated water or food, or modifying forage plants to induce genetic changes when consumed by target animals, and by employing carriers such as liposomes and nanoparticles. The advent of gene editing systems now allows the production of animals that when released into the environment will drive the desired genetic trait (gene drive) through wild populations over time via reproduction. These new tools present issues of both positive and unintended negative environmental impacts that have often not yet been encountered by wildlife managers. The flow of modified genes through the environment and the potential for negative effects, perhaps irreversible, must be understood before these tools are widely used. Thus, regulatory mechanisms must be in place adequately assess potential harm. Three genetic-based tool case studies (recombinant RNA (rRNA), silencing RNA (siRNA), gene drive) will be presented as examples of the unique challenges these new management tools present for traditional assessments of environmental hazards by regulatory agencies. In addition, the current regulatory authorities and processes will be discussed to provide some context as to how the U.S. is regulating these products.
4:00PM Steps for Using Genetic Technologies Successfully in Conservation and Wildlife Management Situations
  Kara Laney
Emerging genetic technologies such as CRISPR hold great promise as new tools to manage human-wildlife conflict, invasive species, and species loss. The successful application of these technologies will require their deployment to be context-specific, accounting for the complexities of environmental change, community ecology, and public opinion. This presentation will build on the conclusions and recommendations of recent National Academies of Sciences, Engineering, and Medicine (NASEM) consensus reports on biotechnology products, gene drives, and livestock-wildlife management. It will also draw upon ongoing NASEM studies of biodiversity conservation in coral reefs and North American forests. The work of committees with diverse expertise, these reports and studies suggest that emerging genetic technologies can play an important role in combating threats to biodiversity. To be most effective, conservation management products and approaches derived from these technologies need to be tested iteratively at scales of increasing complexity (laboratory, field trial, ecosystem). They also need to be subjected to rigorous ecological risk assessment. Decisions to use emerging genetic technologies should weigh the potential benefits against the possible costs of deployment and evaluate these tradeoffs in comparison to other management options. Finally, emerging genetic technologies will likely need to be used in combination with more traditional tools and approaches for addressing conservation and resource management problems. As novel technologies, the use of emerging genetic technologies should be done in consultation with stakeholders and interested and affected parties. Strategies of public engagement should be tailored appropriately for different audiences and should evolve as technologies and human sensibilities change.
4:20PM Ecological Risk Assessment of Genetic Technologies for Wildlife Management
  Caroline E. Ridley; Glenn W. Suter; Meridith Fry; Jeffry L. Dean
The options to control and potentially eradicate harmful pests, wildlife diseases, and invasive species using genetic manipulation are rapidly developing. Emerging products such as pesticide sprays that contain RNA as the active ingredient, genetically engineered sterile insects, and gene drive organisms may soon be available to wildlife managers to improve the environment and conservation outcomes. It remains important, however, to understand both the benefits and potential harms of these technologies. Ecological risk assessment is the framework used to evaluate potential adverse ecological effects from exposure to one or more stressors. This approach has been widely used for evaluating conventional pesticides and now is being adapted to newer technologies (i.e., genetically engineered mosquitoes that suppress population size). Among the products that will challenge the applicability and completeness of current approaches are gene drive organisms, as they possess novel attributes that will surely influence the characterization of risk. In this context, we identify three main areas that warrant further consideration as they fall outside the scope of traditional ecological risk assessment. First, gene drive organisms are designed to modify wild populations over the course of successive generations. This means various evolutionary and population-level processes will affect the genotypic makeup and phenotypic nature of the product. Second, variation in genotype and phenotype of the product in the environment could result in complex or unexpected non-target effects. Third, gene drive organisms are designed to spread modified traits through populations and to withstand time. This raises the possibility that, absent functional spatial or temporal controls, non-target effects could be spatially extensive and long-lasting. Herein, we will highlight areas of research that could help assess the risk of gene drive products. Disclaimer: The views expressed here are those of the authors and do not represent the official views of the US EPA.
4:40PM Social License and Advanced Genetic Technologies
  Stas Burgiel
Increasingly, genetic tools are being used to detect and solve pressing environmental, social, and health-related challenges. Rapid technology development in this field is also challenging the application of regulatory regimes, which are themselves working to adapt to a growing field of advanced genetic technology applications and players. These changes are taking place in the context of broader skepticism of both scientific and regulatory institutions and their abilities to align with public interests. While the other presentations in this session focus on the technical and scientific aspects of advanced genetic technologies, this presentation will address the sociopolitical context for their application to invasive species problems. Social license refers to public acceptance of a particular set of practices by a business or entity. Explicitly this covers public engagement around the general development of advanced genetic technologies as well as their application or release in specific sites. Underlying that level of social exchange is the presumption that such technologies have also gone through appropriate regulatory channels that ensure they meet existing safety standards for public and environmental health. This presentation will focus on these inter-related aspects of policy and social acceptance in the context of invasive species control and management. From a policy perspective this will include recent efforts to adapt the federal regulatory framework, its potential scope, as well as key challenges and limitations. From a social perspective this will look at broader efforts to inform and educate the public, as well as the need for more specific outreach and consultation with communities and other stakeholders potentially affected by the use of these technologies to address invasive species and their impacts.

 
Organizers: Larry Clark, USDA-APHIS-WS-National Wildlife Research Center, Fort Collins, CO
 
Supported by: Wildlife Services

Symposium
Location: Cleveland CC Date: October 8, 2018 Time: 12:50 pm - 5:00 pm