Conservation Genomics of Threatened Animal Species

Steiner, Cynthia C.; Putnam, Andrea S.; Hoeck, Paquita E. A.; Ryder, Oliver A.

doi:10.1146/annurev-animal-031412-103636

Cited by 136 publications

(114 citation statements)

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“…The decreasing cost of biotechnology, in particular HTS, has enabled functional genomic analysis of species of conservation interest using approaches previously limited to model organisms (Steiner et al 2013). Practical applications include identification of adaptive or fitness-related loci, monitoring loci related to stress events, and describing the molecular basis of inbreeding depression (Schwartz et al 2007;Paige 2010).…”

Section: Functional Genetics and Genomicsmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

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Section: Functional Genetics and Genomicsmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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“…Numerous reviews have covered these advancements in relation to conservation in detail [6,20,[28][29][30][31][32][33], and novel techniques and analyses are still emerging (Box 1). It is fair to say, however, that to date conservation genomics and the 90 broader fields of ecological and evolutionary genomics are far from mature.…”

Section: Scaling-up: What Can Genomics Do For Conservation Genetics?mentioning

confidence: 99%

Genomics and the challenging translation into conservation practice

Shafer¹,

Wolf²,

Alves³

et al. 2015

Trends in Ecology & Evolution

460

470

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The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

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“…Lacy 2012 ;Steiner et al 2013 ). These genomic tools can assist in identifying and determining what resources to conserve and through what methods.…”

Section: Discussionmentioning

confidence: 99%

The Role of Genomics in Conservation and Reproductive Sciences

Johnson

Koepfli

2014

Reproductive Sciences in Animal Conservation

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Genomics, the study of an organism's genome through DNA analyses, is a central part of the biological sciences and is rapidly changing approaches to animal conservation. The genomes of thousands of organisms, including vertebrates, invertebrates, and plants have been sequenced and the results annotated, augmented and refined through the application of new approaches in transcriptomics, proteomics, and metabolomics that enhance the characterization of messenger RNA, proteins, and metabolites. The same computational advances that are catalyzing "-omic" technologies and novel approaches to address fundamental research questions are facilitating bioinformatic analysis and enabling access of primary and derivative data and results in public and private databases (Zhao and Grant. Curr Pharm Biotechnol 12:293-305, 2011). These tools will be used to provide fundamental advances in our understanding of reproductive biology across vertebrate species and promise to revolutionize our approach to conservation biology.The vulnerability of animal populations and their genetic diversity is well documented, as are the myriad of causes and threats to their persistence, including habitat degradation and loss, overexploitation, pollution, invasive alien species, and climate change. Of the 64,283 vertebrates assessed by the International Union for Conservation of Nature in their 2012 Red List of Threatened Species, 7,250 or ~11 % are threatened with extinction, a percentage that has been increasing steadily for at least the last decade ( www.iucnredlist.org ). Among many of these species, important genetic diversity has been lost, thereby increasing their vulnerability as genetically diverse populations have higher fitness, generally are more resilient to environmental challenges, and have more adaptive potential (Reed and Frankham Conserv Biol 17:230-237, 2003; Luikart et al. Nat Rev Genet 4:981-994, 2003). In turn, genetic variation within and among populations may be essential to maintaining functional ecosystems, evolutionary process and will impact future food supplies, human health, biomaterial development and geopolitics (Myers and Knoll Proc Natl Acad Sci U S A 98:5389-5392, 2001; Templeton et al. Proc Natl Acad Sci U S A 98:5426-5432, 2001). Therefore, conservation of genetic diversity is a social, cultural, scientific, and economic prerogative and is the key to adaptation in the uncertain future of a human-dominated environment. Once lost, genetic resources are nearly impossible to regain, increasing the urgency of fundamental global approaches (e.g. www.cbd.int/sp/targets ).In this chapter we provide a review of current research and recent advances in biotechnology and genomic approaches for animal conservation and the management of genetic resources, with an emphasis on reproductive sciences. It is intended to provide information and insights for research and to provoke thoughts on how to take advantage of these opportunities.

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Conservation Genomics of Threatened Animal Species

Cited by 136 publications

References 152 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

Genomics and the challenging translation into conservation practice

The Role of Genomics in Conservation and Reproductive Sciences

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