Is It Time for Synthetic Biodiversity Conservation?

Plant conservation in the age of genome editing: opportunities and challenges

Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.

A link between evolution and society fostering the UN sustainable development goals

Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.

Potential distribution patterns and species richness of avifauna in rapidly urbanizing East China

In recent years, increased species extinction and habitat loss have significantly reduced biodiversity, posing a serious threat to both nature and human survival. Environmental factors strongly influence bird distribution and diversity. The potential distribution patterns and species richness offer a conservation modeling framework for policymakers to assess the effectiveness of natural protected areas (PAs) and optimize their existing ones. Very few such studies have been published that cover a large and complete taxonomic group with fine resolution at regional scale. Here, using birds as a study group, the maximum entropy model (MaxEnt) was used to analyze the pattern of bird species richness in Jiangsu Province. Using an unparalleled amount of occurrence data, we created species distribution models (SDMs) for 312 bird species to explore emerging diversity patterns at a resolution of 1 km2. The gradient of species richness is steep, decreasing sharply away from water bodies, particularly in the northern part of Jiangsu Province. The migratory status and feeding habits of birds also significantly influence the spatial distribution of avian species richness. This study reveals that the regions with high potential bird species richness are primarily distributed in three areas: the eastern coastal region, the surrounding area of the lower reaches of the Yangtze River, and the surrounding area of Taihu Lake. Compared with species richness hotspots and existing PAs, we found that the majority of hotspots are well-protected. However, only a small portion of the regions, such as coastal areas of Sheyang County in Yancheng City, as well as some regions along the Yangtze River in Nanjing and Zhenjiang, currently have relatively weak protection. Using stacked SDMs, our study reveals effective insights into diversity patterns, directly informing conservation policies and contributing to macroecological research advancements.

Gene drives for the extinction of wild metapopulations

Population-suppressing gene drives may be capable of extinguishing wild populations, with proposed applications in conservation, agriculture, and public health. However, unintended and potentially disastrous consequences of release of drive-engineered individuals are extremely difficult to predict. We propose a model for the dynamics of a sex ratio-biasing drive, and using simulations, we show that failure of the suppression drive is often a natural outcome due to stochastic and spatial effects. We further demonstrate rock-paper-scissors dynamics among wild-type, drive-infected, and extinct populations that can persist for arbitrarily long times. Gene drive-mediated extinction of wild populations entails critical complications that lurk far beyond the reach of laboratory-based studies. Our findings help in addressing these challenges.

Attackers gain the upper hand over plants in the face of rapid global change

Interactions among organisms in natural ecosystems are the foundational underpinnings of nearly all ecological studies. It has never been more important to increase our awareness of how these interactions are altered by human activity, threatening biodiversity and disrupting ecosystem functioning. Much of the historic focus of species conservation has been the preservation of endangered and endemic species at risk from hunting, over-exploitation, and habitat destruction. However, there is increasing evidence that differences between plants and their attacking organisms in the speed and direction of physiological, demographic, and genetic (adaptation) responses to global change are having devastating consequences, resulting in large-scale losses of dominant or abundant plant species, particularly in forest ecosystems. From the elimination in the wild of the American chestnut to the extensive regional damage caused by insect outbreaks in temperate forest ecosystems, these losses of dominant species change the ecological landscape and functioning, and represent important threats to biodiversity at all scales. Introductions due to human activity, range shifts due to climate change, and their combination are the principal drivers behind these profound ecosystem changes. In this Review, we argue that there is an urgent need to increase our recognition and hone our predictive power for how these imbalances may occur. Moreover, we should seek to minimize the consequences of these imbalances in order to ensure the preservation of the structure, function and biodiversity of entire ecosystems, not just rare or highly endangered species.

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Understanding Local Adaptation to Prepare Populations for Climate Change

Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.

Direct and indirect impacts of synthetic biology on biodiversity conservation

The world's biodiversity is in crisis. Synthetic biology has the potential to transform biodiversity conservation, both directly and indirectly, in ways that are negative and positive. However, applying these biotechnology tools to environmental questions is fraught with uncertainty and could harm cultures, rights, livelihoods, and nature. Decisions about whether or not to use synthetic biology for conservation should be understood alongside the reality of ongoing biodiversity loss. In 2022, the 196 Parties to the United Nations Convention on Biological Diversity are negotiating the post-2020 Global Biodiversity Framework that will guide action by governments and other stakeholders for the next decade to conserve the worlds' biodiversity. To date, synthetic biologists, conservationists, and policy makers have operated in isolation. At this critical time, this review brings these diverse perspectives together and emerges out of the need for a balanced and inclusive examination of the potential application of these technologies to biodiversity conservation.

How public values for threatened species are affected by conservation strategies

While the imminent extinction of many species is predicted, prevention is expensive, and decision-makers often have to prioritise funding. In democracies, it can be argued that conservation using public funds should be influenced by the values placed on threatened species by the public, and that community views should also affect the conservation management approaches adopted. We conducted on online survey with 2400 respondents from the general Australian public to determine 1) the relative values placed on a diverse set of 12 threatened Australian animal species and 2) whether those values changed with the approach proposed to conserve them. The survey included a contingent valuation and a choice experiment. Three notable findings emerged: 1) respondents were willing to pay $60/year on average for a species (95% confidence interval: $23 to $105) to avoid extinction in the next 20 years based on the contingent valuation, and $29 to $100 based on the choice experiment, 2) respondents were willing to pay to reduce the impact of feral animals on almost all presented threatened species, 3) for few species and respondents, WTP was lower when genetic modification to reduce inbreeding in the remaining population was proposed.

Network-level containment of single-species bioengineering

Ecological systems are facing major diversity losses in this century owing to Anthropogenic effects. Habitat loss, overexploitation of resources, invasion and pollution are rapidly jeopardizing the survival of whole communities. It has been recently suggested that a potential approach to flatten the curve of species extinction and prevent catastrophic shifts would involve the engineering of one selected species within one of these communities. Such possibility has started to become part of potential intervention scenarios to preserve biodiversity. Despite its potential, very little is known about the actual dynamic responses of complex ecological networks to the introduction of a synthetic strains derived from a resident species. In this paper, we address this problem by modelling the response of a community to the addition of a synthetic strain derived from a member of a stable ecosystem. We show that the community interaction matrix largely limits the spread of the engineered strain, thus suggesting that species diversity acts as an ecological firewall. The implications for future scenarios of ecosystem engineering are outlined. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Ecological complexity and the biosphere: the next 30 years

Global warming, habitat loss and overexploitation of limited resources are leading to alarming biodiversity declines. Ecosystems are complex adaptive systems that display multiple alternative states and can shift from one to another in abrupt ways. Some of these tipping points have been identified and predicted by mathematical and computational models. Moreover, multiple scales are involved and potential mitigation or intervention scenarios are tied to particular levels of complexity, from cells to human–environment coupled systems. In dealing with a biosphere where humans are part of a complex, endangered ecological network, novel theoretical and engineering approaches need to be considered. At the centre of most research efforts is biodiversity, which is essential to maintain community resilience and ecosystem services. What can be done to mitigate, counterbalance or prevent tipping points? Using a 30-year window, we explore recent approaches to sense, preserve and restore ecosystem resilience as well as a number of proposed interventions (from afforestation to bioengineering) directed to mitigate or reverse ecosystem collapse. The year 2050 is taken as a representative future horizon that combines a time scale where deep ecological changes will occur and proposed solutions might be effective.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Ecological firewalls for synthetic biology

It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while-when required-preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined.

Selfish migrants: How a meiotic driver is selected to increase dispersal

Meiotic drivers are selfish genetic elements that manipulate meiosis to increase their transmission to the next generation to the detriment of the rest of the genome. One example is the t haplotype in house mice, which is a naturally occurring meiotic driver with deleterious traits—poor fitness in polyandrous matings and homozygote inviability or infertility—that prevent its fixation. Recently, we discovered and validated a novel effect of t in a long‐term field study on free‐living wild house mice and with experiments: t‐carriers are more likely to disperse. Here, we ask what known traits of the t haplotype can select for a difference in dispersal between t‐carriers and wildtype mice. To that end, we built individual‐based models with dispersal loci on the t and the homologous wildtype chromosomes. We also allow for density‐dependent expression of these loci. The t haplotype consistently evolves to increase the dispersal propensity of its carriers, particularly at high densities. By examining variants of the model that modify different costs caused by t, we show that the increase in dispersal is driven by the deleterious traits of t, disadvantage in polyandrous matings and lethal homozygosity or male sterility. Finally, we show that an increase in driver‐carrier dispersal can evolve across a range of values in driver strength and disadvantages.

Genetic approaches for increasing fitness in endangered species

The global rate of wildlife extinctions is accelerating, and the persistence of many species requires conservation breeding programs. A central paradigm of these programs is to preserve the genetic diversity of the founder populations. However, this may preserve original characteristics that make them vulnerable to extinction. We introduce targeted genetic intervention (TGI) as an alternative approach that promotes traits that enable species to persist in the face of threats by changing the incidence of alleles that impact on fitness. The TGI toolkit includes methods with established efficacy in model organisms and agriculture but are largely untried for conservation, such as synthetic biology and artificial selection. We explore TGI approaches as a species-restoration tool for intractable threats including infectious disease and climate change.

Generation of Gene Drive Mice for Invasive Pest Population Suppression

Gene drives are genetic elements that are transmitted to greater than 50% of offspring and have potential for population modification or suppression. While gene drives are known to occur naturally, the recent emergence of CRISPR-Cas9 genome-editing technology has enabled generation of synthetic gene drives in a range of organisms including mosquitos, flies, and yeast. For example, studies in Anopheles mosquitos have demonstrated >95% transmission of CRISPR-engineered gene drive constructs, providing a possible strategy for malaria control. Recently published studies have also indicated that it may be possible to develop gene drive technology in invasive rodents such as mice. Here, we discuss the prospects for gene drive development in mice, including synthetic "homing drive" and X-shredder strategies as well as modifications of the naturally occurring t haplotype. We also provide detailed protocols for generation of gene drive mice through incorporation of plasmid-based transgenes in a targeted and non-targeted manner. Importantly, these protocols can be used for generating transgenic mice for any project that requires insertion of kilobase-scale transgenes such as knock-in of fluorescent reporters, gene swaps, overexpression/ectopic expression studies, and conditional "floxed" alleles.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

What is the role of zooxanthellae during coral bleaching? Review of zooxanthellae and their response to environmental stress

Coral reefs are diverse and productive but sensitive ecosystems. Due to the impact of climate change, these organisms are in danger of dying out, mainly through the process of coral bleaching, which is the process by which zooxanthellae (algal endosymbionts) are expelled from their respective coral hosts, causing the coral to lose colour and become white. Coral bleaching has been linked to increases in sea surface temperatures as well as an increase in light intensity. We reviewed the different zooxanthellae taxa and their ecological traits, as well as the information available on the protective mechanisms present in zooxanthellae cells when they experience environmental stress conditions, such as temperature fluctuations, specifically concentrating on heat shock proteins and their response to antioxidant stress. The eight clades (A–H) previously recognised were reorganised into seven existing genera. Different zooxanthellae taxa exhibit different ecological traits such as their photosynthetic stress responses to light and temperature. Zooxanthellae have the ability to regulate the number and type of heat shock proteins (Hsps) they produce during a heat response. They can also regulate the host’s respective Hsps. Antioxidant responses that can prevent coral hosts from expelling the zooxanthellae, can be found both within exposed coral tissue and the zooxanthellae cells. Despite the lower likelihood of bleaching in South African coral reefs, genetic engineering presents a useful tool to understand and adapt traits within zooxanthellae genotypes to help mitigate coral bleaching in the future.

Genomic Approaches for Conservation Management in Australia under Climate Change

Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.

A sliver of the past: The decimation of the genetic diversity of the Mexican wolf

The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.

Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive

Introduced rodent populations pose significant threats worldwide, with particularly severe impacts on islands. Advancements in genome editing have motivated interest in synthetic gene drives that could potentially provide efficient and localized suppression of invasive rodent populations. Application of such technologies will require rigorous population genomic surveys to evaluate population connectivity, taxonomic identification, and to inform design of gene drive localization mechanisms. One proposed approach leverages the predicted shifts in genetic variation that accompany island colonization, wherein founder effects, genetic drift, and island-specific selection are expected to result in locally fixed alleles (LFA) that are variable in neighboring nontarget populations. Engineering of guide RNAs that target LFA may thus yield gene drives that spread within invasive island populations, but would have limited impacts on nontarget populations in the event of an escape. Here we used pooled whole-genome sequencing of invasive mouse (Mus musculus) populations on four islands along with paired putative source populations to test genetic predictions of island colonization and characterize locally fixed Cas9 genomic targets. Patterns of variation across the genome reflected marked reductions in allelic diversity in island populations and moderate to high degrees of differentiation from nearby source populations despite relatively recent colonization. Locally fixed Cas9 sites in female fertility genes were observed in all island populations, including a small number with multiplexing potential. In practice, rigorous sampling of presumptive LFA will be essential to fully assess risk of resistance alleles. These results should serve to guide development of improved, spatially limited gene drive design in future applications.

Combining the responses of habitat suitability and connectivity to climate change for an East Asian endemic frog

Background

Understanding the impacts of past and contemporary climate change on biodiversity is critical for effective conservation. Amphibians have weak dispersal abilities, putting them at risk of habitat fragmentation and loss. Both climate change and anthropogenic disturbances exacerbate these risks, increasing the likelihood of additional amphibian extinctions in the near future. The giant spiny frog (Quasipaa spinosa), an endemic species to East Asia, has faced a dramatic population decline over the last few decades. Using the giant spiny frog as an indicator to explore how past and future climate changes affect landscape connectivity, we characterized the shifts in the suitable habitat and habitat connectivity of the frog.

Results

We found a clear northward shift and a reduction in the extent of suitable habitat during the Last Glacial Maximum for giant spiny frogs; since that time, there has been an expansion of the available habitat. Our modelling showed that “overwarm” climatic conditions would most likely cause a decrease in the available habitat and an increase in the magnitude of population fragmentation in the future. We found that the habitat connectivity of the studied frogs will decrease by 50–75% under future climate change. Our results strengthen the notion that the mountains in southern China and the Sino-Vietnamese transboundary regions can act as critical refugia and priority areas of conservation planning going forward.

Conclusions

Given that amphibians are highly sensitive to environmental changes, our findings highlight that the responses of habitat suitability and connectivity to climate change can be critical considerations in future conservation measures for species with weak dispersal abilities and should not be neglected, as they all too often are.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12983-021-00398-w.

Genetic mixing for population management: From genetic rescue to provenancing

Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Designing gene drives to limit spillover to non-target populations

The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene-drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives—field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications.

CRISPR-based gene drive is an emerging genetic engineering technology that enables engineered genetic variants, which are usually designed to be harmful to the organism carrying them, to be spread rapidly in populations. Although this technology is promising for controlling disease vectors and invasive species, there is a considerable risk that a gene drive could unintentionally spillover from the target population, where it was deployed, to non-target populations. We develop mathematical models of gene-drive dynamics that incorporate migration between target and non-target populations to investigate the possibility of effectively applying a gene drive in the target population while limiting its spillover to non-target populations (‘differential targeting’). We observe that the feasibility of differential targeting depends on the gene-drive design specification, as well as on the migration rates between the populations. Even when differential targeting is possible, as migration increases, the possibility for differential targeting disappears. We find that differential targeting can be effective for low migration rates, and that it is sensitive to the design of the gene drive under high migration rates. We suggest that differential targeting could be used, in combination with other mitigation measures, as an additional safeguard to limit gene drive spillovers.

Global Governing Bodies: A Pathway for Gene Drive Governance for Vector Mosquito Control

Gene drive technologies represent powerful tools to develop vector control strategies that will complement the current approaches to mitigate arthropod-borne infectious diseases. The characteristics of gene drive technologies have raised additional concerns to those for standard genetically engineered organisms. This generates a need for adaptive governance that has not been met yet because of the rapid rate of progress in gene drive research. For the eventual release of gene drive insects into wild populations, an international governance network would be helpful in guiding scientists, stakeholders, public opinion, and affected communities in its use. We examined the current institutions and governing bodies among various continents that could have an impact on gene drive governance or the potential to adapt to its future use. Possible governance strategies also are proposed that seek to bridge gaps and promote an ethically sound policy framework. Ideally, governance strategies should be developed before or at the same pace as gene drive research to anticipate field releases and maximize their impact as a public health tool. However, this is not likely to happen as it takes years to develop global accords, and some countries may choose to move ahead independently on the new technology.

Polyandry blocks gene drive in a wild house mouse population

Gene drives are genetic elements that manipulate Mendelian inheritance ratios in their favour. Understanding the forces that explain drive frequency in natural populations is a long-standing focus of evolutionary research. Recently, the possibility to create artificial drive constructs to modify pest populations has exacerbated our need to understand how drive spreads in natural populations. Here, we study the impact of polyandry on a well-known gene drive, called t haplotype, in an intensively monitored population of wild house mice. First, we show that house mice are highly polyandrous: 47% of 682 litters were sired by more than one male. Second, we find that drive-carrying males are particularly compromised in sperm competition, resulting in reduced reproductive success. As a result, drive frequency decreased during the 4.5 year observation period. Overall, we provide the first direct evidence that the spread of a gene drive is hampered by reproductive behaviour in a natural population.

This study resolves a long-standing mystery of why t haplotypes, an example of selfish genes, have persisted at unexpectedly low frequencies in wild mouse populations. It shows that multiple mating by females, which is more common at higher mouse population densities, decreases the frequency of driving t haplotypes.

Creating proxies of extinct species: the bioethics of de-extinction

In April 2013 the National Geographic magazine carried the cover title 'Reviving extinct species, we can, but should we?' suggesting that the technical challenges had been met, but some ethical concerns remained unresolved. Seven years later it is clear that this is not the case. Here we consider the technical scope, the uncertainties, and some of the bioethical issues raised by the future prospect of de-extinction. Biodiversity and welfare will not always align, and when a clash is unavoidable, a trade-off will be necessary, seeking the greatest overall value. De-extinction challenges our current conservation mind-set that seeks to preserve the species and population diversity that currently exists. But if we want to sustain and enhance a biodiverse natural world we might have to be forward looking and embrace the notion of bio-novelty by focussing more on ecosystem stability and resilience, rather than backward looking and seeking to try and recreate lost worlds.

Resistance to natural and synthetic gene drive systems

Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general.

The potential for a CRISPR gene drive to eradicate or suppress globally invasive social wasps

CRISPR gene drives have potential for widespread and cost-efficient pest control, but are highly controversial. We examined a potential gene drive targeting spermatogenesis to control the invasive common wasp (Vespula vulgaris) in New Zealand. Vespula wasps are haplodiploid. Their life cycle makes gene drive production challenging, as nests are initiated by single fertilized queens in spring followed by several cohorts of sterile female workers and the production of reproductives in autumn. We show that different spermatogenesis genes have different levels of variation between introduced and native ranges, enabling a potential 'precision drive' that could target the reduced genetic diversity and genotypes within the invaded range. In vitro testing showed guide-RNA target specificity and efficacy that was dependent on the gene target within Vespula, but no cross-reactivity in other Hymenoptera. Mathematical modelling incorporating the genetic and life history traits of Vespula wasps identified characteristics for a male sterility drive to achieve population control. There was a trade-off between drive infiltration and impact: a drive causing complete male sterility would not spread, while partial sterility could be effective in limiting population size if the homing rate is high. Our results indicate that gene drives may offer viable suppression for wasps and other haplodiploid pests.

Making sense of nature conservation after the end of nature

The concept of nature in Western thought has been informed by the assumption of a categorical distinction between natural and artificial entities, which goes back to John Stuart Mill or even Aristotle. Such a way of articulating the natural/artificial distinction has proven unfit for conservation purposes mainly because of the extent and the pervasiveness of human activities that would leave no nature left to be conserved, and alternative views have been advanced. In this contribution, after arguing for the importance of the concept of naturalness as a guide for conservation, I will try to provide an account of the natural/artificial distinction suited to contemporary conservation framing. Focusing on a particular kind of objects that I suggest to name "environmental objects", I propose and defend the view of "naturalness as independence" according to which the more or less an environmental object's identity conditions and survival depend on human intervention, the more or less that object is artificial or natural, respectively. According to this view, conserving environmental objects will equate to maintaining or improving their naturalness (vis-à-vis their artefactualness) or even originating artificial objects that may become new natural objects. This view has the advantage, on the one hand, of providing a rationale for a distinction which is not only part of how people think, but also pervasive in conservation practices and policies and, on the other hand, of accounting for the global pervasiveness of human intervention in the so-called natural world.

Regulation of Synthetic Biology: Developments Under the Convention on Biological Diversity and Its Protocols

The primary international forum deliberating the regulation of "synthetic biology" is the Convention on Biological Diversity (CBD), along with its subsidiary agreements concerned with the biosafety of living modified organisms (LMOs; Cartagena Protocol on Biosafety to the CBD), and access and benefit sharing in relation to genetic resources (Nagoya Protocol to the CBD). This discussion has been underway for almost 10 years under the CBD agenda items of "synthetic biology" and "new and emerging issues relating to the conservation and sustainable use of biological diversity," and more recently within the scope of Cartagena Protocol topics including risk assessment and risk management, and "digital sequence information" jointly with the Nagoya Protocol. There is no internationally accepted definition of "synthetic biology," with it used as an umbrella term in this forum to capture "new" biotechnologies and "new" applications of established biotechnologies, whether actual or conceptual. The CBD debates are characterized by polarized views on the adequacy of existing regulatory mechanisms for "new" types of LMOs, including the scope of the current regulatory frameworks, and procedures and tools for risk assessment and risk mitigation and/or management. This paper provides an overview of international developments in biotechnology regulation, including the application of the Cartagena Protocol and relevant policy developments, and reviews the development of the synthetic biology debate under the CBD and its Protocols, including the major issues expected in the lead up to and during the 2020 Biodiversity Conference.

The ethics of genetic engineering and gene drives in conservation

The ethical issues associated with using genetic engineering and gene drives in conservation are typically described as consisting of risk assessment and management, public engagement and acceptance, opportunity costs, risk and benefit distributions, and oversight. These are important, but the ethical concerns extend beyond them because the use of genetic engineering has the potential to significantly alter the practices, concepts, and value commitments of conservation. I sought to elucidate the broader set of ethical issues connected with a potential genetic engineering turn in conservation and provide an approach to ethical analysis of novel conservation technologies. The primary rationales offered in support of using genetic engineering and gene drives in conservation are efficiency and necessity for achieving conservation goals. The instrumentalist ethical perspective associated with these rationales involves assessing novel technologies as a means to accomplish desired ends. For powerful emerging technologies the instrumentalist perspective needs to be complemented by a form-of-life perspective frequently applied in the philosophy of technology. The form-of-life perspective involves considering how novel technologies restructure the activities into which they are introduced. When the form-of-life perspective is applied to creative genetic engineering in conservation, it brings into focus a set of ethical issues, such as those associated with power, meaning, relationships, and values, that are not captured by the instrumentalist perspective. It also illuminates why the use of gene drives in conservation is so ethically and philosophically interesting.

Ex situ collections and their potential for the restoration of extinct plants

The alarming current and predicted species extinction rates have galvanized conservationists in their efforts to avoid future biodiversity losses, but for species extinct in the wild, few options exist. We posed the questions, can these species be restored, and, if so, what role can ex situ plant collections (i.e., botanic gardens, germplasm banks, herbaria) play in the recovery of plant genetic diversity? We reviewed the relevant literature to assess the feasibility of recovering lost plant genetic diversity with using ex situ material and the probability of survival of subsequent translocations. Thirteen attempts to recover species extinct in the wild were found, most of which used material preserved in botanic gardens (12) and seed banks (2). One case of a locally extirpated population was recovered from herbarium material. Eight (60%) of these cases were successful or partially successful translocations of the focal species or population; the other 5 failed or it was too early to determine the outcome. Limiting factors of the use of ex situ source material for the restoration of plant genetic diversity in the wild include the scarcity of source material, low viability and reduced longevity of the material, low genetic variation, lack of evolution (especially for material stored in germplasm banks and herbaria), and socioeconomic factors. However, modern collecting practices present opportunities for plant conservation, such as improved collecting protocols and improved cultivation and storage conditions. Our findings suggest that all types of ex situ collections may contribute effectively to plant species conservation if their use is informed by a thorough understanding of the aforementioned problems. We conclude that the recovery of plant species currently classified as extinct in the wild is not 100% successful, and the possibility of successful reintroduction should not be used to justify insufficient in situ conservation.

Transforming ecology and conservation biology through genome editing

As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.

The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles

Selfish genetic elements have been found in the genomes of many species, yet our understanding of their evolutionary dynamics is only partially understood. A number of distinct selfish Medea elements are naturally present in many populations of the red flour beetle (Tribolium castaneum). Although these Medea elements are predicted by models to increase in frequency within populations because any offspring of a Medea-bearing mother that do not inherit at least one Medea allele will die, experiments demonstrating an increase in a naturally occurring Medea element are lacking. Our survey of the specific Medea element, M1, in the United States showed that it had a patchy geographic distribution. From the survey, it could not be determined if this distribution was caused by a slow process of M1 colonization of discrete populations or if some populations lacked M1 because they had genetic factors conferring resistance to the Medea mechanism. We show that populations with naturally low to intermediate M1 frequencies likely represent transient states during the process of Medea spread. Furthermore, we find no evidence that genetic factors are excluding M1 from US populations where the element is not presently found. We also show how a known suppressor of Medea can impair the increase of M1 in populations and discuss the implications of our findings for pest-management applications of Medea elements.

Technology innovation: advancing capacities for the early detection of and rapid response to invasive species

The 2016–2018National Invasive Species Council (NISC) Management Plan and Executive Order 13751 call for US federal agencies to foster technology development and application to address invasive species and their impacts. This paper complements and draws on an Innovation Summit, review of advanced biotechnologies applicable to invasive species management, and a survey of federal agencies that respond to these high-level directives. We provide an assessment of federal government capacities for the early detection of and rapid response to invasive species (EDRR) through advances in technology application; examples of emerging technologies for the detection, identification, reporting, and response to invasive species; and guidance for fostering further advancements in applicable technologies. Throughout the paper, we provide examples of how federal agencies are applying technologies to improve programmatic effectiveness and cost-efficiencies. We also highlight the outstanding technology-related needs identified by federal agencies to overcome barriers to enacting EDRR. Examples include improvements in research facility infrastructure, data mobilization across a wide range of invasive species parameters (from genetic to landscape scales), promotion of and support for filling key gaps in technological capacity (e.g., portable, field-ready devices with automated capacities), and greater investments in technology prizes and challenge competitions.

The distribution and spread of naturally occurring Medea selfish genetic elements in the United States

Selfish genetic elements (SGEs) are DNA sequences that are transmitted to viable offspring in greater than Mendelian frequencies. Medea SGEs occur naturally in some populations of red flour beetle (Tribolium castaneum) and are expected to increase in frequency within populations and spread among populations. The large-scale U.S. distributions of Medea-4 (M4) had been mapped based on samples from 1993 to 1995. We sampled beetles in 2011-2014 and show that the distribution of M4 in the United States is dynamic and has shifted southward. By using a genetic marker of Medea-1 (M1), we found five unique geographic clusters with high and low M1 frequencies in a pattern not predicted by microsatellite-based analysis of population structure. Our results indicate the absence of rigid barriers to Medea spread in the United States, so assessment of what factors have limited its current distribution requires further investigation. There is great interest in using synthetic SGEs, including synthetic Medea, to alter or suppress pest populations, but there is concern about unpredicted spread of these SGEs and potential for populations to become resistant to them. The finding of patchy distributions of Medea elements suggests that released synthetic SGEs cannot always be expected to spread uniformly, especially in target species with limited dispersal.

Public views about editing genes in wildlife for conservation

Developments in CRISPR-based gene-editing technologies have generated a growing number of proposals to edit genes in wildlife to meet conservation goals. As these proposals have attracted greater attention, controversies have emerged among scientists and stakeholder groups over potential consequences and ethical implications of gene editing. Responsible governance cannot occur without consulting broader publics, yet little effort has been made to systematically assess public understandings and beliefs in relation to this new area of applied genetic engineering. We analyzed data from a survey of U.S. adults (n = 1600), collected by YouGov, and that examined respondents' concerns about gene editing in animal and plant wildlife and how those concerns are shaped by cultural dispositions toward science and beliefs about the appropriateness of intervening in nature at the genetic level. On average, respondents perceived more risk than benefit in using these tools. Over 70% agreed that gene editing in wildlife could be "easily used for the wrong purposes." When evaluating the moral acceptability of gene editing in wildlife, respondents evaluated applications to improve survival in endangered wildlife as more morally acceptable than applications to decrease abundance in a population or eliminate a population. Belief in the authority of scientific knowledge was positively related to favorable views of the benefits, risks, and moral acceptability of editing genes in wildlife. The belief that editing genes in wildlife inappropriately intervenes in nature predicted relatively more concern about risks and moral acceptability and skepticism about benefits. Given high levels of concern and skepticism about gene editing in wildlife for conservation among the U.S. public, a take-it-slow approach to making decisions about when or whether to use these tools is advisable. Early opinions, including those uncovered in this study, are likely to be provisional. Thus, consulting the public should be an ongoing process.

Rodent gene drives for conservation: opportunities and data needs

Invasive rodents impact biodiversity, human health and food security worldwide. The biodiversity impacts are particularly significant on islands, which are the primary sites of vertebrate extinctions and where we are reaching the limits of current control technologies. Gene drives may represent an effective approach to this challenge, but knowledge gaps remain in a number of areas. This paper is focused on what is currently known about natural and developing synthetic gene drive systems in mice, some key areas where key knowledge gaps exist, findings in a variety of disciplines relevant to those gaps and a brief consideration of how engagement at the regulatory, stakeholder and community levels can accompany and contribute to this effort. Our primary species focus is the house mouse, Mus musculus, as a genetic model system that is also an important invasive pest. Our primary application focus is the development of gene drive systems intended to reduce reproduction and potentially eliminate invasive rodents from islands. Gene drive technologies in rodents have the potential to produce significant benefits for biodiversity conservation, human health and food security. A broad-based, multidisciplinary approach is necessary to assess this potential in a transparent, effective and responsible manner.

Evolution in the Anthropocene: Informing Governance and Policy

The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.

Assisted Evolution in Astrobiology-Convergence of Ecology and Evolutionary Biology within the Context of Planetary Colonization

In ecology and conservation biology, the concept of assisted evolution aims at the optimization of the resilience of organisms and populations to changing environmental conditions. What has hardly been considered so far is that this concept is also relevant for future astrobiological research, since in artificial extraterrestrial habitats (e.g., plants and insects in martian greenhouses) novel environmental conditions will also affect the survival and performance of organisms. The question therefore arises whether and how space-relevant organisms can be artificially adapted to the desired circumstances in advance. Based on several adaptation and acclimatization strategies in wild ecosystems of Earth, I discuss which methods can be considered for assisted evolution in the context of astrobiological research. This includes enhanced selective breeding, induction of epigenetic inheritance, and genetic engineering, as well as possible problems of these applications. This short overview article aims to stimulate an emerging discussion as to whether humans, which are already prominent drivers of Earth's evolution, should consider such interventions for future planetary colonization as well.