A conservation genomics workflow to guide practical management actions

Despite the promising applications of genome-wide information to conservation, the field of conservation genomics remains hindered by a research-practice gap. Identifying the benefits from genomics in relation to fish conservation planning and decision-making could contribute to bridging this gap. The goals of our study were twofold. First, we reviewed the fish conservation genomic literature to determine how genomic information has been used to inform conservation decision making; and second, we examined how genomic information can be linked to an existing conservation decision framework. Our review showed that, as fish conservation genomics studies accumulate over time, collaborations between researchers and conservation practitioners are becoming increasingly frequent. While the field is dominated by studies of economically important families (e.g. salmonids, acipenserids) in first-world countries (North America, Europe), it has a broad taxonomic coverage where species of both local and global conservation concern are well represented. We also show that genomic information can readily be harnessed to guide decisions within existing conservation decision frameworks, from the conceptualization (identification of conservation targets and threats) to the implementation and the monitoring of conservation actions. In addition, our review identifies some limitations related to genomic inferences for conservation and proposes solutions to address these uncertainties and improve communication between conservation genomic scientists and practitioners. For genomic researchers, we outline how conservation decisions are made; for practitioners, we illustrate how genomic information can inform decision-making.

Let's Move toward Genomics for Butterfly Ecology and Insect Conservation

Understanding in the evolutionary processes, endangered mechanisms, and adaptive evolution history are key scientific issues in conservation biology. During the past decades, advances in high-throughput sequencing and multi-disciplinary crossover have triggered the development of conservation genomics, which refers to the use of new genomic technologies and genomic information in solving the existing problems in conservation biology. Conservation genomics mainly focuses on the endangered mechanism and conservation strategies aiming at protection of survivability and diversity of endangered species. Application of conservation genomics into the study of endanger plant species has provided innovated protection concept for biologists and promoted the development of population-based conservation strategies. This chapter summarizes the studies of population genomics for agronomically and commercially important plants threatened and endangered, discusses the advantages of conservation genomics for the analysis of genetic diversity, inferences about the history of population dynamics, evaluation of natural forces on wild plant populations, and the establishment of effective conservation strategies. This chapter also presents the development trends in genomics for the conservation of endangered plant species.

Conservation genetics and genomics of threatened vertebrates in China

It is important for emerging conservation practitioners to gain experience in the use of evidence-based practices, by way of critical analysis and understanding of the context and application of conservation actions. We developed a learning activity based on the use of evidence-based decision-making in sea turtle conservation. The prompts build conservation science literacy as learners identify published methods to assess risks and mitigate threats. A practical exercise asks learners to assess threats at different locations and propose the most appropriate protection strategy. The activity familiarizes learners with decisions and challenges common to conservationists.

This thesis examined if signals of selection are present in the bottlenecked and reintroduced populations of the Alpine ibex (Capra ibex). By utilizing single nucleotide polymorphism (SNP) data, I identified weak signals of purifying selection and positive selection. Furthermore, I quantified the detection accuracy achievable for studies using genetic outliers or associations among allele frequencies and environmental variables to detect positive selection after a bottleneck. Additionally, I discussed the biases present in a high-throughput sequencing dataset due to batch effects that can arise in long-term studies where sequencing data is added incrementally. Finally, in this thesis I discussed the importance of considering genetics when planning the reintroduction of a species. Population bottlenecks can have profound and long-lasting genetic consequences. Due to their reduced effective population size, bottlenecked species experience strong genetic drift, loss of genetic variation, and increased inbreeding. They are therefore at risk of maladaptation and extinction. Despite these risks examples of thriving bottlenecked populations are known. Outside of conservation biology, population bottlenecks are important evolutionary forces because they can affect the rate and direction of adaptation. As a result, identifying examples of selection after a bottleneck is of importance to evolutionary and conservation biology. In this thesis, I utilised genome-wide SNP data for 27 populations of Alpine ibex, including the remnant population in the Gran Paradiso National Park. This data was generated with restriction site associated DNA sequencing (RADseq). RADseq is a high-throughput sequencing method that sequences genomic DNA around a restriction enzyme site. I identified over 6000 SNPs in the Alpine ibex genome. With this data, I identified putative signals of purifying selection by comparing exonic SNPs, which are likely under selection, with intronic SNPs and SNPs in intergenic regions, that are expected to be largely neutral. Furthermore I examined the ratio of non-synonymous to synonymous sites. The heterozygosity of exonic SNPs was significantly below that of introns and of intergenic SNPs. In addition, the ratio of non-synonymous to synonymous sites was below one. While this suggests purifyingii selection, due to marker and test limitations, these results are not conclusive and the presence of purifying selection should be viewed with caution. I then searched for signals of positive selection by scanning for large differences in allele frequencies among populations and for correlations between allele frequencies and an environmental variable. The high rates of genetic drift in bottlenecked populations can create false signals of positive selection when using such methods. Therefore, I used a population genetic (forward-time) simulation approach that followed Alpine ibex demography, to generate a simulated set of SNPs including neutral loci and loci that were under selection. I then used these loci to quantify the accuracy of three selection detection methods. To this end, I examined the number of false positive neutral SNPs identified by each method, as well as the number of true positive and false negative simulated selected SNPs. I found that a true discovery rate of over 70% can be achieved by combining three selection detection methods to identify “triple positive” SNPs, and an environmental correlation detection approach. When I applied the selection detection methods to the Alpine ibex empirical RADseq dataset no triple positive SNPs were identified by the triple positive environmental correlation approach. Thus there are no SNPs I confidently identified as under selection, though weak candidates were found by the lower accuracy methods (30- 50% true discovery rate) that may be suitable for further examination. High-throughput sequencing is maturing and an increasing number of studies have used data obtained over time or generated by different investigators. In this thesis, I also discuss the biases and errors, so-called ‘batch effects’, that can be introduced into a study if subsets of data differ in how they were obtained and contain different technical artefacts. I present a case study in the Alpine ibex where batch effects lead to a misleading biological conclusion. Finally in an additional co-authored publication, the importance of considering the long-term genetics of a population during a reintroduction was presented and discussed.

Conservation genetics is an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity. In recent years, the field has been expanding due to advances in technologies and related disciplines, including genomics. Genomics is the study of the structure, function, and evolution of genomes—the entire collection of hereditary information for a given organism—as well as interactions between genes. This essay collection is excerpted from Conservation Genetics in the Age of Genomics (2009, Columbia University Press). The selected essays provide an introduction to challenges faced in conservation genetics and conservation biology in general, and examine how developments in genomics might provide advances in conservation genetics. This first chapter reviews the integration of genetics into conservation biology and discusses several areas in which genetics can aid in conservation decision-making. This text is distributed in this form by the Network of Conservation Educators and Practitioners (NCEP) with permission from the authors and publishers.

Conservation genetics is an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity. In recent years, the field has been expanding due to advances in technologies and related disciplines, including genomics. Genomics is the study of the structure, function, and evolution of genomes—the entire collection of hereditary information for a given organism—as well as interactions between genes. This essay collection is excerpted from Conservation Genetics in the Age of Genomics (2009, Columbia University Press). The selected essays provide an introduction to challenges faced in conservation genetics and conservation biology in general, and examine how developments in genomics might provide advances in conservation genetics. This first chapter reviews the integration of genetics into conservation biology and discusses several areas in which genetics can aid in conservation decision-making. This text is distributed in this form by the Network of Conservation Educators and Practitioners (NCEP) with permission from the authors and publishers.

One of the most fundamental aims in conservation is to ensure the long-term persistence of biodiversity. To achieve this goal, hundreds of thousands of protected areas have been set aside globally to buffer species from anthropogenic impacts and provide a platform for management actions. To be effective, protected areas must preserve existing patterns of biodiversity (e.g. species, ecosystems) and also the evolutionary that create new patterns of biodiversity. By ensuring that disruptions to evolutionary are minimized, protected areas can help maintain existing patterns of genetic diversity and facilitate adaptation to new threats. This is particularly important in a world where environmental change is rapidly accelerating. However, despite this, evolutionary are rarely considered when siting new protected areas or evaluating existing protected area systems.The main goal of this thesis is to improve our understanding of how evolutionary can be incorporated into conservation planning to deliver more effective protected areas. To achieve this goal, I develop a novel decision support tool to target intra-specific variation in conservation prioritizations (Chapter 2). I then investigate potential surrogates for representing intra-specific genetic variation (Chapter 3) and maintaining gene flow in prioritizations (Chapter 4). Finally, I evaluate how well the existing protected area system is representing adaptive for nearly every vertebrate species on Earth (Chapter 5).Building prioritizations that conserve evolutionary has been a long standing challenge in conservation planning. In Chapter 2, I develop a new decision support tool---the raptr R package---for generating multi-species prioritizations that minimize the overall cost of the solution whilst (i) securing a representative sample of the intra-specific variation for each species, (ii) providing an adequate amount of habitat for each species, and (iii) minimizing the level of overall fragmentation in the solution. By applying this method to simulated and case-study species, I show that conservation planners need to explicitly target intra-specific variation---otherwise they risk losing it. This chapter paves the way for using intra-specific variation to guide the selection of nature reserves. After developing this decision support tool, I use it to examine potential surrogates for conserving evolutionary processes.One of the reasons that evolutionary are not often used to guide reserve selection is that substantial resources and expertise are needed to obtain and analyze genetic data. In Chapters 3 and 4, I investigate the effectiveness of strategies for capturing evolutionary using freely available genetic data for multiple alpine plant species. In Chapter 3, I show that prioritizations capturing a representative sample of the climatic variation and geographic spread across species' distributions tend also to capture a large proportion of species' adaptive and neutral genetic variation. In Chapter 4, I found that conventional approaches for increasing connectivity may not actually result in prioritizations that maintain strong levels of gene flow. These findings illustrate how genetic data can be used to guide conservation planning. Furthermore, they show that freely available data can, at least in some cases, be used to deliver effective protected area systems even when genetic data are not available. After demonstrating that environmental data can be used as a surrogate for conserving evolutionary processes, I then use environmental data to explore how well the existing global protected area system is conserving adaptive evolutionary processes.In response to the biodiversity crisis, 195 governments have signed the Convention on Biological Diversity. These nations have pledged to protect at least 17 % of the Earth's land and improve the conservation status for species at risk of extinction by the year 2020 (Aichi Targets 11 and 12). One of the components for monitoring progress made towards conserving biodiversity is the protection of habitats that contain key evolutionary processes (Annex I). By conserving populations in a wide range of climatic conditions, protected area systems can maximize the range of existing and potential local adaptations within a species. In Chapter 5, I discover that the global protected area system poorly represents the climatic conditions found across species' geographic distributions. To begin to address this shortfall, I also identify priority areas for protected area expansion. This work provides the first global assessment for how well protected areas are fostering adaptive evolutionary process for the world's amphibians, birds, and mammals.This thesis sheds new light on understanding how well evolutionary are conserved, and how conservation decisions can be made in a way that safeguards evolutionary processes. It combines ideas from conservation biology, decision science, and evolutionary biology. The discoveries made here will be relevant to a broad range of scientists working in conservation and genetics research, and also policy makers and planners engaged in protecting biodiversity. Careful utilization of the decision support tool (Chapter 2), genetic and surrogate data (Chapters 3 and 4), and priority areas (Chapter 5) outlined in this thesis could substantially increase the chances for the long-term persistence of biodiversity.

Although the application of population and evolutionary genetic theory and methods to address issues of conservation relevance has a long history, the formalization of conservation genetics as a research field is still relatively recent. One of the periodic catalysts for increased research effort in the field has been advances in molecular technologies, leading to an increasingly wider variety of molecular markers for application in conservation genetic studies. To date, genetic methods have been applied in conservation biology primarily as selectively neutral molecular tools for resolving questions of conservation relevance. However, there has been renewed interest in complementing the analysis of neutral markers with the assessment of loci that may be directly involved in responses to processes such as environmental change, with a view to identifying the genes involved in them. These kinds of studies are now possible due to the increase in availability of genomic resources for nonmodel organisms, and there will likely be an even more rapid increase in the near future due to the advent of new ultrahigh throughput-sequencing technologies. This review considers the implications of the most recent developments in genomic technologies and their potential for contributing to the conservation of populations and species. Three "conservation genomics" case studies are presented (Atlantic salmon, Salmo sala; the butterfly, Melitaea cinxia; and the California condor, Gymnogyps californianus) in order to demonstrate the diversity of applications now possible. While it is clear that genomics approaches in conservation will not replace other tried-and-true methods, these recent developments open up an exciting new range of possibilities that will enable further diversification of the application of genomics in conservation biology.

Global expansion of lighting and noise pollution alters how animals receive and interpret environmental cues. However, we lack a cross-taxon understanding of how animal traits influence species vulnerability to this growing phenomenon. This knowledge is needed to improve the design and implementation of policies that mitigate or reduce sensory pollutants. We present results from an expert knowledge survey that quantified the relative influence of 21 ecological, anatomical, and physiological traits on the vulnerability of terrestrial vertebrates to elevated levels of anthropogenic lighting and noise. We aimed not only to quantify the importance of threats and the relative influence of traits as viewed by sensory and wildlife experts, but to examine knowledge gaps based on the variation in responses. Identifying traits that had less consensus can guide future research for strengthening ecologists' and conservation biologists' understanding of sensory abilities. Our findings, based on 280 responses of expert opinion, highlight the increasing recognition among experts that sensory pollutants are important to consider in management and conservation decisions. Participant responses show mounting threats to species with narrow niches; especially habitat specialists, nocturnal species, and those with the greatest ability to differentiate environmental visual and auditory cues. Our results call attention to the threat specialist species face and provide a generalizable understanding of which species require additional considerations when developing conservation policies and mitigation strategies in a world altered by expanding sensory pollutant footprints. We provide a step-by-step example for translating these results to on-the-ground conservation planning using two species as case studies.

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

Response of ecological storage and conservation to land use transformation: A case study of a mining town in China

We devised a participatory modeling approach for setting management thresholds that show when management intervention is required to address undesirable ecosystem changes. This approach was designed to be used when management thresholds: must be set for environmental indicators in the face of multiple competing objectives; need to incorporate scientific understanding and value judgments; and will be set by participants with limited modeling experience. We applied our approach to a case study where management thresholds were set for a mat-forming brown alga, Hormosira banksii, in a protected area management context. Participants, including management staff and scientists, were involved in a workshop to test the approach, and set management thresholds to address the threat of trampling by visitors to an intertidal rocky reef. The approach involved trading off the environmental objective, to maintain the condition of intertidal reef communities, with social and economic objectives to ensure management intervention was cost-effective. Ecological scenarios, developed using scenario planning, were a key feature that provided the foundation for where to set management thresholds. The scenarios developed represented declines in percent cover of H. banksii that may occur under increased threatening processes. Participants defined 4 discrete management alternatives to address the threat of trampling and estimated the effect of these alternatives on the objectives under each ecological scenario. A weighted additive model was used to aggregate participants' consequence estimates. Model outputs (decision scores) clearly expressed uncertainty, which can be considered by decision makers and used to inform where to set management thresholds. This approach encourages a proactive form of conservation, where management thresholds and associated actions are defined a priori for ecological indicators, rather than reacting to unexpected ecosystem changes in the future.

国土空间生态修复与保护空间识别——以北京市为例